diff --git a/CHANGELOG.md b/CHANGELOG.md index 66662e0c..d12c7a6b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#243](https://github.com/genomic-medicine-sweden/nallo/pull/243) - Added nf-test to the short variant annotation workflow - [#245](https://github.com/genomic-medicine-sweden/nallo/pull/245) - Added repeat annotation with Stranger - [#252](https://github.com/genomic-medicine-sweden/nallo/pull/252) - Added a new `SCATTER_GENOME` subworkflow +- [#255](https://github.com/genomic-medicine-sweden/nallo/pull/255) - Added a new `RANK_VARIANTS` subworkflow to rank SNVs using genmod ### `Changed` diff --git a/README.md b/README.md index 8a832c6b..e666837e 100644 --- a/README.md +++ b/README.md @@ -44,9 +44,9 @@ 1. Annotate variants with database(s) of choice, i.e. [gnomAD](https://gnomad.broadinstitute.org), [CADD](https://cadd.gs.washington.edu) etc. ([`echtvar`](https://github.com/brentp/echtvar)) 2. Annotate variants ([`VEP`](https://github.com/Ensembl/ensembl-vep)) -##### Filtering +##### Filtering and ranking -- TBD +- Rank variants [GENMOD](https://github.com/Clinical-Genomics/genmod) ## Usage diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index 6ef9313b..f1af5c06 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,3 +1,3 @@ sample,file,family_id,paternal_id,maternal_id,sex,phenotype -sample_1,/path/to/fastq_or_bam/files/sample_1.fastq.gz,FAM,PAT,MAT,0,1 -sample_2,/path/to/fastq_or_bam/files/sample_2.bam,FAM,PAT,MAT,1,1 +sample_1,/path/to/fastq_or_bam/files/sample_1.fastq.gz,FAM,0,0,0,2 +sample_2,/path/to/fastq_or_bam/files/sample_2.bam,FAM,0,0,1,1 diff --git a/assets/schema_input.json b/assets/schema_input.json index 269a3085..63c61f99 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -28,13 +28,13 @@ "paternal_id": { "type": "string", "pattern": "^\\S+$", - "errorMessage": "Paternal ID must be provided and cannot contain spaces. If no paternal ID is available, use any ID not in sample column.", + "errorMessage": "Paternal ID must be provided and cannot contain spaces. If no paternal ID is available, use 0.", "meta": ["paternal_id"] }, "maternal_id": { "type": "string", "pattern": "^\\S+$", - "errorMessage": "Maternal ID must be provided and cannot contain spaces. If no maternal ID is available, use any ID not in sample column.", + "errorMessage": "Maternal ID must be provided and cannot contain spaces. If no maternal ID is available, use 0.", "meta": ["maternal_id"] }, "sex": { diff --git a/bin/add_most_severe_consequence.py b/bin/add_most_severe_consequence.py new file mode 100755 index 00000000..cb1538c7 --- /dev/null +++ b/bin/add_most_severe_consequence.py @@ -0,0 +1,192 @@ +#!/usr/bin/env python3 + +# Written by Ramprasad Neethiraj and released under the MIT license. +# See git repository (https://github.com/nf-core/raredisease) for full license text. + +import argparse +import gzip +import sys +from pathlib import Path +from typing import Tuple, TextIO + + +def parse_vep_csq_transcripts( + transcripts: list, allele_ind: int, csq_ind: int, hgnc_ind: int, var_csq: list +) -> Tuple[list, list, list, list]: + """ + Parse conseqences for each transcript and return HGNC IDs, alleles, and their severity rank + based on the term's ranking in the ensembl consequences list. + + Args: + transcripts (list): A list of vep transcript annotation + allele_ind (int) : Index of the "allele" in the vep annotation record + csq_ind (int) : Index of the "Consequence" in the vep annotation record + hgnc_ind (int) : Index of the "HGNC_ID" in the vep annotation record + var_csq (list): A list of consequence terms ordered by rank + + Returns: + hgnc_ids (list): list of hgnc ids in the record + alleles (list): list of alleles in the record + consequences (list): list of consequence terms in the record + severity (list): list of consequence term ranks + """ + + consequences = [] + hgnc_ids = [] + severity = [] + alleles = [] + for transcript in transcripts: + vep_fields = transcript.strip().split("|") + csq = vep_fields[csq_ind].split("&")[0] + hgnc_id = vep_fields[hgnc_ind] + allele = vep_fields[allele_ind].replace("CSQ=", "") + consequences.append(csq) + hgnc_ids.append(hgnc_id) + severity.append(var_csq.index(csq)) + alleles.append(allele) + return hgnc_ids, alleles, consequences, severity + + +def construct_most_severe_consequence_info( + line: str, allele_ind: int, csq_ind: int, hgnc_ind: int, var_csq: list +) -> list: + """ + Parse conseqences for each transcript and return HGNC IDs, alleles, and their severity rank + based on the term's ranking in the ensembl consequences list. + + Args: + line (str) : Vcf record + allele_ind (int) : Index of the "allele" in the vep annotation record + csq_ind (int) : Index of the "Consequence" in the vep annotation record + hgnc_ind (int) : Index of the "HGNC_ID" in the vep annotation record + var_csq (list): A list of consequence terms ordered by rank + + Returns: + columns (list): A list of fields in the vcf record with most severe consequence added + to the INFO column + """ + + columns = line.strip().split() + info_fields = columns[7].split(";") + for field in info_fields: + if field.startswith("CSQ="): + transcripts = field.split("CSQ=")[1].split(",") + hgnc_ids, alleles, consequences, severity = parse_vep_csq_transcripts( + transcripts, allele_ind, csq_ind, hgnc_ind, var_csq + ) + unique_ids = list(set(hgnc_ids)) + mscsq_anno = [] + for gene_id in unique_ids: + if gene_id != "": + indices = find_indices(hgnc_ids, gene_id) + alleles_sub = [alleles[i] for i in indices] + consequences_sub = [consequences[i] for i in indices] + severity_sub = [severity[i] for i in indices] + most_severe_csq = consequences_sub[severity_sub.index(min(severity_sub))] + most_severe_allele = alleles_sub[severity_sub.index(min(severity_sub))] + mscsq_anno.append(gene_id + ":" + most_severe_allele + "|" + most_severe_csq) + if mscsq_anno: + columns[7] += ";most_severe_consequence=" + ",".join(mscsq_anno) + return columns + + +def find_indices(list_to_check: list, item_to_find: str) -> list: + """ + Get indices of an element in a list + + Args: + list_to_check (list) + item_to_find (value) + + Returns: + indices (list) + """ + indices = [] + for idx, value in enumerate(list_to_check): + if value == item_to_find: + indices.append(idx) + return indices + + +def parse_vep_csq_schema(line: str) -> Tuple[int, int, int]: + """ + Get indices of allele, consequence, and hgnc id in the annotation + + Args: + line: INFO line in the vcf header with CSQ information + + Returns: + allele_ind (int) : Index of the "allele" in the vep annotation record + csq_ind (int) : Index of the "Consequence" in the vep annotation record + hgnc_ind (int) : Index of the "HGNC_ID" in the vep annotation record + """ + fields = line.strip().split("Format: ")[1].replace('">', "").split("|") + allele_ind = fields.index("Allele") + csq_ind = fields.index("Consequence") + hgnc_ind = fields.index("HGNC_ID") + + return allele_ind, csq_ind, hgnc_ind + + +def write_csq_annotated_vcf(file_in: TextIO, file_out: TextIO, var_csq: list): + """Add most severe consequence field to record, and write the record to a vcf file""" + for line in file_in: + if line.startswith("#"): + file_out.write(line) + if line.startswith("##INFO=\n' + ) + else: + mscsq = construct_most_severe_consequence_info(line, allele_ind, csq_ind, hgnc_ind, var_csq) + file_out.write("\t".join(mscsq) + "\n") + + +def parse_args(argv=None): + """Define and immediately parse command line arguments.""" + parser = argparse.ArgumentParser( + description="Annotate vcf with the most severe consequence field.", + epilog="Example: python vcfparser.py --file_in vep.vcf --file_out vep.most_severe_csq.vcf --variant_csq variant_consequence.txt", + ) + parser.add_argument( + "--file_in", + metavar="FILE_IN", + type=Path, + help="Vcf file annotated with vep.", + ) + parser.add_argument( + "--file_out", + metavar="FILE_OUT", + type=Path, + help="Vcf with most_severe_consequence annotations added to it.", + ) + parser.add_argument( + "--variant_csq", + metavar="VARIANT_CSQ", + type=Path, + help="Variant consequences ranked by severity", + ) + return parser.parse_args(argv) + + +def main(argv=None): + """Coordinate argument parsing and program execution.""" + args = parse_args(argv) + if not args.file_in.is_file(): + print(f"The given input file {args.file_in} was not found!") + sys.exit(2) + if not args.variant_csq.is_file(): + print(f"The given variant consequence file {args.variant_csq} was not found!") + sys.exit(2) + args.file_out.parent.mkdir(parents=True, exist_ok=True) + with open(args.variant_csq) as f: + var_csq = [line.strip() for line in f] + opener = gzip.open if (args.file_in.suffix == ".gz") else open + with open(args.file_out, "w") as out_vcf: + with opener(args.file_in, "rt") as in_vcf: + write_csq_annotated_vcf(in_vcf, out_vcf, var_csq) + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/bin/add_most_severe_pli.py b/bin/add_most_severe_pli.py new file mode 100755 index 00000000..b578fe28 --- /dev/null +++ b/bin/add_most_severe_pli.py @@ -0,0 +1,129 @@ +#!/usr/bin/env python3 + +# Written by Ramprasad Neethiraj and released under the MIT license. +# See git repository (https://github.com/nf-core/raredisease) for full license text. + +import argparse +import gzip +import sys +from pathlib import Path +from typing import TextIO + + +def parse_vep_transcripts(transcripts: list, pli_ind: int) -> list: + """ + Parse each transcript and return a list of pli values. + + Args: + transcripts (list): A list of vep transcript annotation + pli_ind (int) : Index of pli value in the vep annotation record + + Returns: + pli_values (list): list of pli values in the record + """ + + pli_values = [] + for transcript in transcripts: + vep_fields = transcript.strip().split("|") + pli_value = vep_fields[pli_ind] + pli_values.append(pli_value) + return pli_values + + +def construct_most_severe_pli_info(line: str, pli_ind: int) -> list: + """ + Parse gene symbols, find the highest pli value of all gene symbols, add most_severe_pli tag to the info + field and return a list of modified columns + + Args: + line (str) : Vcf record + pli_ind (int) : Index of pli value in the vep annotation record + + Returns: + columns (list): A list of fields in the vcf record with most severe pli added + to the INFO column + """ + + columns = line.strip().split() + info_fields = columns[7].split(";") + for field in info_fields: + if field.startswith("CSQ="): + transcripts = field.split("CSQ=")[1].split(",") + break + pli_values = parse_vep_transcripts(transcripts, pli_ind) + try: + pli_max = max(pli_values) + except ValueError: + pli_max = "" + if pli_max: + columns[7] += ";most_severe_pli={:.2f}".format(float(pli_max)) + return columns + + +def parse_vep_csq_schema(line: str) -> int: + """ + Get indices of gene symbol in the annotation + + Args: + line: INFO line in the vcf header with CSQ information + + Returns: + pli_ind (int) : Index of pli value in the vep annotation record + """ + fields = line.strip().split("Format: ")[1].replace('">', "").split("|") + pli_ind = fields.index("pLI_gene_value") + + return pli_ind + + +def write_pli_annotated_vcf(file_in: TextIO, file_out: TextIO): + """Add most severe pli field to record, and write the record to a vcf file""" + for line in file_in: + if line.startswith("#"): + file_out.write(line) + if line.startswith("##INFO=\n' + ) + else: + vcf_record = construct_most_severe_pli_info(line, pli_ind) + file_out.write("\t".join(vcf_record) + "\n") + + +def parse_args(argv=None): + """Define and immediately parse command line arguments.""" + parser = argparse.ArgumentParser( + description="Annotate vcf with the most severe pli field.", + epilog="Example: python vcfparser.py --file_in vep.vcf --file_out vep.most_severe_pli.vcf", + ) + parser.add_argument( + "--file_in", + metavar="FILE_IN", + type=Path, + help="Vcf file annotated with vep's pli plugin.", + ) + parser.add_argument( + "--file_out", + metavar="FILE_OUT", + type=Path, + help="Vcf with most_severe_pli annotations added to it.", + ) + return parser.parse_args(argv) + + +def main(argv=None): + """Coordinate argument parsing and program execution.""" + args = parse_args(argv) + if not args.file_in.is_file(): + print(f"The given input file {args.file_in} was not found!") + sys.exit(2) + args.file_out.parent.mkdir(parents=True, exist_ok=True) + opener = gzip.open if (args.file_in.suffix == ".gz") else open + with open(args.file_out, "w") as out_vcf: + with opener(args.file_in, "rt") as in_vcf: + write_pli_annotated_vcf(in_vcf, out_vcf) + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/conf/modules/annotate_consequence_pli.config b/conf/modules/annotate_consequence_pli.config new file mode 100644 index 00000000..3158c4f4 --- /dev/null +++ b/conf/modules/annotate_consequence_pli.config @@ -0,0 +1,32 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = Conditional clause +---------------------------------------------------------------------------------------- +*/ + +process { + withName: '.*:ANN_CSQ_PLI_SNV:.*' { + publishDir = [ + enabled: false + ] + } + + withName: '.*ANN_CSQ_PLI_SNV:ADD_MOST_SEVERE_CSQ' { + ext.prefix = { "${meta.id}_snv_csq" } + } + + withName: '.*ANN_CSQ_PLI_SNV:ADD_MOST_SEVERE_PLI' { + ext.prefix = { "${meta.id}_snv_csq_pli" } + } + + withName: '.*ANN_CSQ_PLI_SNV:TABIX_BGZIPTABIX' { + ext.prefix = { "${meta.id}_snv_csq_pli" } + } +} diff --git a/conf/modules/rank_variants.config b/conf/modules/rank_variants.config new file mode 100644 index 00000000..379eb62f --- /dev/null +++ b/conf/modules/rank_variants.config @@ -0,0 +1,64 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = Conditional clause +---------------------------------------------------------------------------------------- +*/ + +// +// Score and rank SNVs +// + +process { + + withName: '.*:RANK_VARIANTS_SNV:GENMOD_ANNOTATE' { + ext.prefix = { "${meta.id}_snv_genmod_annotate" } + ext.args = { [ + '--annotate_regions', + '--genome-build 38', + '--temp_dir ./' + ].join(' ') } + } + + withName: '.*:RANK_VARIANTS_SNV:GENMOD_MODELS' { + ext.prefix = { "${meta.id}_snv_genmod_models" } + ext.args = "--whole_gene --temp_dir ./" + } + + withName: '.*:RANK_VARIANTS_SNV:GENMOD_SCORE' { + ext.prefix = { "${meta.id}_snv_genmod_score" } + ext.args = "--rank_results" + } + + withName: '.*:RANK_VARIANTS_SNV:GENMOD_COMPOUND' { + ext.prefix = { "${meta.id}_snv_genmod_compound" } + ext.args = "--temp_dir ./" + } + + withName: '.*:RANK_VARIANTS_SNV:BCFTOOLS_SORT' { + ext.when = false + } + + withName: '.*:RANK_VARIANTS_SNV:TABIX_BGZIP' { + ext.prefix = { "${meta.id}_snv_ranked" } + publishDir = [ + path: { "${params.outdir}/ranked_variants" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: '.*:RANK_VARIANTS_SNV:TABIX_TABIX' { + publishDir = [ + path: { "${params.outdir}/ranked_variants" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } +} diff --git a/conf/test.config b/conf/test.config index d1f927f7..0bbf6994 100644 --- a/conf/test.config +++ b/conf/test.config @@ -43,6 +43,11 @@ params { vep_cache = params.pipelines_testdata_base_path + 'nallo/reference/vep_cache_test_data.tar.gz' snp_db = params.pipelines_testdata_base_path + 'nallo/testdata/snp_dbs.csv' + // Rank variants + reduced_penetrance = params.pipelines_testdata_base_path + 'nallo/reference/reduced_penetrance.tsv' + score_config_snv = params.pipelines_testdata_base_path + 'nallo/reference/rank_model_snv.ini' + variant_consequences_snv = params.pipelines_testdata_base_path + 'nallo/reference/variant_consequences_v2.txt' + // Somalier somalier_sites = params.pipelines_testdata_base_path + 'nallo/reference/somalier_sites.vcf.gz' diff --git a/docs/output.md b/docs/output.md index 232a5214..013a9eba 100644 --- a/docs/output.md +++ b/docs/output.md @@ -23,6 +23,7 @@ - [Repeat calling](#repeat-calling) - [Repeat annotation](#repeat-annotation) - [SNV Annotation](#snv-annotation) + - [Ranked Variants](#ranked-variants) - [SNV Calling](#snv-calling) ## Pipeline overview @@ -295,6 +296,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ ### SNV Annotation [echtvar](https://github.com/brentp/echtvar) and [VEP](https://www.ensembl.org/vep) is used to annotate small variants. +In case of affected samples, [echtvar](https://github.com/brentp/echtvar) and [VEP](https://www.ensembl.org/vep) is used to annotate small variants.
Output files from SNV Annotation @@ -306,6 +308,23 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ - `*.vcf.gz.tbi`: Index of the corresponding VCF file
+### Ranked variants + +#### Filter_vep + +[filter_vep from VEP](https://www.ensembl.org/info/docs/tools/vep/script/vep_filter.html) is used to subset the variants based on a list of HGNC ID:s. Typical use case is that you want to filter your results to only include variants in a predefined set of clinically relevant genes. This step is optional and can be disabled by using the flag `--skip_vep_filter`. You will always get the complete VCF together with the clinical VCF. + +#### GENMOD + +[GENMOD](https://github.com/Clinical-Genomics/genmod) is a simple to use command line tool for annotating and analyzing genomic variations in the VCF file format. GENMOD can annotate genetic patterns of inheritance in vcf files with single or multiple families of arbitrary size. Each variant will be assigned a predicted pathogenicity score. The score will be given both as a raw score and a normalized score with values between 0 and 1. The tags in the INFO field are `RankScore` and `RankScoreNormalized`. The score can be configured to fit your annotations and preferences by modifying the score config file. + +
+Output files + +- `{outputdir}ranked_variants/` + - `*_snv_ranked.vcf.gz`: file containing SNV annotations with their rank scores (does not include mitochondrial variants). + - `*_snv_ranked.vcf.gz.tbi`: index of the file containing SNV annotations with their rank scores. + ### SNV Calling [Sniffles](https://github.com/fritzsedlazeck/Sniffles) is used to call and merge structural variants. diff --git a/docs/usage.md b/docs/usage.md index e853d06e..2b6a585f 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -59,12 +59,12 @@ You will need to create a samplesheet with information about the samples you wou It has to be a comma-separated file with 6 columns, and a header row as shown in the examples below. `file` can either be a gzipped-fastq file or an aligned or unalinged BAM file (BAM files will be converted to FASTQ and aligned again). -`phenotype` is not used at the moment but still required, set it to `1`. If you don't have related samples, `family_id` could be set to sample name, and `paternal_id` and `maternal_id` to a value that is not another `sample` name. +If you don't have related samples, `family_id` could be set to sample name, and `paternal_id` and `maternal_id` should be set to 0. ```console sample,file,family_id,paternal_id,maternal_id,sex,phenotype -HG002,/path/to/HG002.fastq.gz,FAM,HG003,HG004,1,1 -HG005,/path/to/HG005.bam,FAM,HG003,HG004,2,1 +HG002,/path/to/HG002.fastq.gz,FAM,HG003,0,1,2 +HG003,/path/to/HG003.bam,FAM,0,0,2,1 ``` | Fields | Description | @@ -72,8 +72,8 @@ HG005,/path/to/HG005.bam,FAM,HG003,HG004,2,1 | `sample` | Custom sample name, cannot contain spaces. | | `file` | Absolute path to gzipped FASTQ or BAM file. File has to have the extension ".fastq.gz", .fq.gz" or ".bam". | | `family_id` | "Family ID must be provided and cannot contain spaces. If no family ID is available you can use the same ID as the sample | -| `paternal_id` | Paternal ID must be provided and cannot contain spaces. If no paternal ID is available, use any ID not in sample column. | -| `maternal_id` | Maternal ID must be provided and cannot contain spaces. If no maternal ID is available, use any ID not in sample column. | +| `paternal_id` | Paternal ID must be provided and cannot contain spaces. If no paternal ID is available, use 0. | +| `maternal_id` | Maternal ID must be provided and cannot contain spaces. If no maternal ID is available, use 0. | | `sex` | Sex (0=unknown; 1=male; 2=female). | | `phenotype` | Affected status of patient (0 = missing; 1=unaffected; 2=affected). | @@ -114,8 +114,8 @@ Some workflows require additional files: - If running without `--skip_repeat_annotation`, download a json variant catalog, (e.g. [variant_catalog_grch38.json](https://github.com/Clinical-Genomics/stranger/raw/main/stranger/resources/variant_catalog_grch38.json)) matching your reference genome to supply with `--variant_catalog`. - If running without `--skip_snv_annotation`, download [VEP cache](https://ftp.ensembl.org/pub/release-110/variation/vep/homo_sapiens_vep_110_GRCh38.tar.gz) to supply with `--vep_cache` and prepare a samplesheet with annotation databases ([`echtvar encode`](https://github.com/brentp/echtvar)) to supply with `--snp_db`: - -`snp_dbs.csv` + - If your samplesheet contains at least one affected sample (phenotype = 2), `--reduced_penetrance` (Used by GENMOD while modeling the variants. Contains a list of loci that show [reduced penetrance](https://medlineplus.gov/genetics/understanding/inheritance/penetranceexpressivity/) in people. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/reduced_penetrance.tsv)), `--score_config_snv` (Used by GENMOD for ranking the variants. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/rank_model_snv.ini)) and `--variant_consequences_snv` (File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic and mitochondrial SNVs. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/variant_consequences_v2.txt). You can learn more about these terms [here](https://grch37.ensembl.org/info/genome/variation/prediction/predicted_data.html)) is also required. + `snp_dbs.csv` ``` sample,file diff --git a/modules.json b/modules.json index 672d6df2..88cb96db 100644 --- a/modules.json +++ b/modules.json @@ -84,6 +84,26 @@ "installed_by": ["modules"], "patch": "modules/nf-core/fastqc/fastqc.diff" }, + "genmod/annotate": { + "branch": "master", + "git_sha": "1aba459a6f3528bee806403ae47bea304de26603", + "installed_by": ["modules"] + }, + "genmod/compound": { + "branch": "master", + "git_sha": "1aba459a6f3528bee806403ae47bea304de26603", + "installed_by": ["modules"] + }, + "genmod/models": { + "branch": "master", + "git_sha": "1aba459a6f3528bee806403ae47bea304de26603", + "installed_by": ["modules"] + }, + "genmod/score": { + "branch": "master", + "git_sha": "1aba459a6f3528bee806403ae47bea304de26603", + "installed_by": ["modules"] + }, "gfastats": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", @@ -189,6 +209,11 @@ "git_sha": "4806239588f35d27a95b187b4000d80e15152022", "installed_by": ["modules"] }, + "tabix/bgzip": { + "branch": "master", + "git_sha": "09d3c8c29b31a2dfd610305b10550f0e1dbcd4a9", + "installed_by": ["modules"] + }, "tabix/bgziptabix": { "branch": "master", "git_sha": "09d3c8c29b31a2dfd610305b10550f0e1dbcd4a9", diff --git a/modules/local/add_most_severe_consequence.nf b/modules/local/add_most_severe_consequence.nf new file mode 100644 index 00000000..0c572811 --- /dev/null +++ b/modules/local/add_most_severe_consequence.nf @@ -0,0 +1,45 @@ +process ADD_MOST_SEVERE_CSQ { + tag "$meta.id" + label 'process_low' + + conda "conda-forge::python=3.8.3" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/python:3.8.3' : + 'biocontainers/python:3.8.3' }" + + input: + tuple val(meta), path(vcf) + path (variant_consequences) + + output: + tuple val(meta), path("*.vcf") , emit: vcf + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + add_most_severe_consequence.py --file_in ${vcf} --file_out ${prefix}.vcf --variant_csq ${variant_consequences} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + add_most_severe_consequence: v1.0 + python: \$(python --version | sed 's/Python //g') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}_csq.vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + add_most_severe_consequence: v1.0 + python: \$(python --version | sed 's/Python //g') + END_VERSIONS + """ +} diff --git a/modules/local/add_most_severe_pli.nf b/modules/local/add_most_severe_pli.nf new file mode 100644 index 00000000..f2975a22 --- /dev/null +++ b/modules/local/add_most_severe_pli.nf @@ -0,0 +1,44 @@ +process ADD_MOST_SEVERE_PLI { + tag "$meta.id" + label 'process_low' + + conda "conda-forge::python=3.8.3" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/python:3.8.3' : + 'biocontainers/python:3.8.3' }" + + input: + tuple val(meta), path(vcf) + + output: + tuple val(meta), path("*.vcf") , emit: vcf + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + add_most_severe_pli.py --file_in ${vcf} --file_out ${prefix}.vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + add_most_severe_pli: v1.0 + python: \$(python --version | sed 's/Python //g') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}_pli.vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + add_most_severe_pli: v1.0 + python: \$(python --version | sed 's/Python //g') + END_VERSIONS + """ +} diff --git a/modules/nf-core/genmod/annotate/environment.yml b/modules/nf-core/genmod/annotate/environment.yml new file mode 100644 index 00000000..ac8140fd --- /dev/null +++ b/modules/nf-core/genmod/annotate/environment.yml @@ -0,0 +1,7 @@ +name: genmod_annotate +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::genmod=3.8.2 diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf new file mode 100644 index 00000000..eb161187 --- /dev/null +++ b/modules/nf-core/genmod/annotate/main.nf @@ -0,0 +1,46 @@ +process GENMOD_ANNOTATE { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0': + 'biocontainers/genmod:3.8.2--pyhdfd78af_0' }" + + input: + tuple val(meta), path(input_vcf) + + output: + tuple val(meta), path("*_annotate.vcf"), emit: vcf + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + genmod \\ + annotate \\ + $args \\ + --outfile ${prefix}_annotate.vcf \\ + $input_vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' ) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}_annotate.vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/genmod/annotate/meta.yml b/modules/nf-core/genmod/annotate/meta.yml new file mode 100644 index 00000000..3c876ac5 --- /dev/null +++ b/modules/nf-core/genmod/annotate/meta.yml @@ -0,0 +1,41 @@ +name: "genmod_annotate" +description: for annotating regions, frequencies, cadd scores +keywords: + - annotate + - genmod + - ranking +tools: + - "genmod": + description: "Annotate genetic inheritance models in variant files" + homepage: "https://github.com/Clinical-Genomics/genmod" + documentation: "https://github.com/Clinical-Genomics/genmod" + tool_dev_url: "https://github.com/moonso" + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_vcf: + type: file + description: VCF file + pattern: "*.{vcf}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - vcf: + type: file + description: Annotated VCF file + pattern: "*.{vcf}" +authors: + - "@ramprasadn" +maintainers: + - "@ramprasadn" diff --git a/modules/nf-core/genmod/annotate/tests/main.nf.test b/modules/nf-core/genmod/annotate/tests/main.nf.test new file mode 100644 index 00000000..746de32b --- /dev/null +++ b/modules/nf-core/genmod/annotate/tests/main.nf.test @@ -0,0 +1,34 @@ +nextflow_process { + + name "Test Process GENMOD_ANNOTATE" + script "modules/nf-core/genmod/annotate/main.nf" + process "GENMOD_ANNOTATE" + config "./nextflow.config" + tag "modules" + tag "modules_nfcore" + tag "genmod" + tag "genmod/annotate" + + test("genmod_annotate") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.test_data['homo_sapiens']['illumina']['genmod_vcf_gz'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + {assert process.success}, + {assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.2")} + ) + } + + } + +} diff --git a/modules/nf-core/genmod/annotate/tests/nextflow.config b/modules/nf-core/genmod/annotate/tests/nextflow.config new file mode 100644 index 00000000..a1860460 --- /dev/null +++ b/modules/nf-core/genmod/annotate/tests/nextflow.config @@ -0,0 +1,5 @@ +process{ + withName: GENMOD_ANNOTATE { + ext.args = " --annotate_regions " + } +} diff --git a/modules/nf-core/genmod/annotate/tests/tags.yml b/modules/nf-core/genmod/annotate/tests/tags.yml new file mode 100644 index 00000000..88bb35a1 --- /dev/null +++ b/modules/nf-core/genmod/annotate/tests/tags.yml @@ -0,0 +1,2 @@ +genmod/annotate: + - modules/nf-core/genmod/annotate/** diff --git a/modules/nf-core/genmod/compound/environment.yml b/modules/nf-core/genmod/compound/environment.yml new file mode 100644 index 00000000..1e2561fd --- /dev/null +++ b/modules/nf-core/genmod/compound/environment.yml @@ -0,0 +1,7 @@ +name: genmod_compound +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::genmod=3.8.2 diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf new file mode 100644 index 00000000..1731b722 --- /dev/null +++ b/modules/nf-core/genmod/compound/main.nf @@ -0,0 +1,47 @@ +process GENMOD_COMPOUND { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0': + 'biocontainers/genmod:3.8.2--pyhdfd78af_0' }" + + input: + tuple val(meta), path(input_vcf) + + output: + tuple val(meta), path("*_compound.vcf"), emit: vcf + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + genmod \\ + compound \\ + $args \\ + --processes ${task.cpus} \\ + --outfile ${prefix}_compound.vcf \\ + $input_vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' ) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}_compound.vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/genmod/compound/meta.yml b/modules/nf-core/genmod/compound/meta.yml new file mode 100644 index 00000000..aa5f7da5 --- /dev/null +++ b/modules/nf-core/genmod/compound/meta.yml @@ -0,0 +1,41 @@ +name: "genmod_compound" +description: Score compounds +keywords: + - compound + - genmod + - ranking +tools: + - "genmod": + description: "Annotate genetic inheritance models in variant files" + homepage: "https://github.com/Clinical-Genomics/genmod" + documentation: "https://github.com/Clinical-Genomics/genmod" + tool_dev_url: "https://github.com/moonso" + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_vcf: + type: file + description: VCF file + pattern: "*.{vcf}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] # + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - vcf: + type: file + description: Output VCF file + pattern: "*.{vcf}" +authors: + - "@ramprasadn" +maintainers: + - "@ramprasadn" diff --git a/modules/nf-core/genmod/compound/tests/main.nf.test b/modules/nf-core/genmod/compound/tests/main.nf.test new file mode 100644 index 00000000..cf234186 --- /dev/null +++ b/modules/nf-core/genmod/compound/tests/main.nf.test @@ -0,0 +1,33 @@ +nextflow_process { + + name "Test Process GENMOD_COMPOUND" + script "modules/nf-core/genmod/compound/main.nf" + process "GENMOD_COMPOUND" + tag "modules" + tag "modules_nfcore" + tag "genmod" + tag "genmod/compound" + + test("genmod_compound") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.test_data['homo_sapiens']['genome']['genmod_compound_vcf_mt'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + {assert process.success}, + {assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.2")} + ) + } + + } + +} diff --git a/modules/nf-core/genmod/compound/tests/tags.yml b/modules/nf-core/genmod/compound/tests/tags.yml new file mode 100644 index 00000000..870b35e8 --- /dev/null +++ b/modules/nf-core/genmod/compound/tests/tags.yml @@ -0,0 +1,2 @@ +genmod/compound: + - modules/nf-core/genmod/compound/** diff --git a/modules/nf-core/genmod/models/environment.yml b/modules/nf-core/genmod/models/environment.yml new file mode 100644 index 00000000..62a746c7 --- /dev/null +++ b/modules/nf-core/genmod/models/environment.yml @@ -0,0 +1,7 @@ +name: genmod_models +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::genmod=3.8.2 diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf new file mode 100644 index 00000000..0504574a --- /dev/null +++ b/modules/nf-core/genmod/models/main.nf @@ -0,0 +1,53 @@ +process GENMOD_MODELS { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0': + 'biocontainers/genmod:3.8.2--pyhdfd78af_0' }" + + input: + tuple val(meta), path(input_vcf) + path (fam) + path (reduced_penetrance) + + output: + tuple val(meta), path("*_models.vcf"), emit: vcf + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def family_file = fam ? "--family_file ${fam}" : "" + def pen_file = reduced_penetrance ? "--reduced_penetrance ${reduced_penetrance}" : "" + """ + genmod \\ + models \\ + $args \\ + $pen_file \\ + $family_file \\ + --processes ${task.cpus} \\ + --outfile ${prefix}_models.vcf \\ + $input_vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' ) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}_models.vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/genmod/models/meta.yml b/modules/nf-core/genmod/models/meta.yml new file mode 100644 index 00000000..dd9001e0 --- /dev/null +++ b/modules/nf-core/genmod/models/meta.yml @@ -0,0 +1,49 @@ +name: "genmod_models" +description: annotate models of inheritance +keywords: + - models + - genmod + - ranking +tools: + - "genmod": + description: "Annotate genetic inheritance models in variant files" + homepage: "https://github.com/Clinical-Genomics/genmod" + documentation: "https://github.com/Clinical-Genomics/genmod" + tool_dev_url: "https://github.com/moonso" + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_vcf: + type: file + description: vcf file + pattern: "*.{vcf}" + - reduced_penetrance: + type: file + description: file with gene ids that have reduced penetrance + pattern: "*.{tsv}" + - family_file: + type: file + description: ped file + pattern: "*.{ped}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - vcf: + type: file + description: Output VCF file + pattern: "*.{vcf}" +authors: + - "@ramprasadn" +maintainers: + - "@ramprasadn" diff --git a/modules/nf-core/genmod/models/tests/main.nf.test b/modules/nf-core/genmod/models/tests/main.nf.test new file mode 100644 index 00000000..a69bb136 --- /dev/null +++ b/modules/nf-core/genmod/models/tests/main.nf.test @@ -0,0 +1,35 @@ +nextflow_process { + + name "Test Process GENMOD_MODELS" + script "modules/nf-core/genmod/models/main.nf" + process "GENMOD_MODELS" + tag "modules" + tag "modules_nfcore" + tag "genmod" + tag "genmod/models" + + test("genmod_models") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['illumina']['genmod_annotate_vcf_gz'], checkIfExists: true) + ] + input[1] = file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true) + input[2] = [] + """ + } + } + + then { + assertAll( + {assert process.success}, + {assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.2")} + ) + } + + } + +} diff --git a/modules/nf-core/genmod/models/tests/tags.yml b/modules/nf-core/genmod/models/tests/tags.yml new file mode 100644 index 00000000..72b3b6bb --- /dev/null +++ b/modules/nf-core/genmod/models/tests/tags.yml @@ -0,0 +1,2 @@ +genmod/models: + - modules/nf-core/genmod/models/** diff --git a/modules/nf-core/genmod/score/environment.yml b/modules/nf-core/genmod/score/environment.yml new file mode 100644 index 00000000..bacc4cec --- /dev/null +++ b/modules/nf-core/genmod/score/environment.yml @@ -0,0 +1,7 @@ +name: genmod_score +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::genmod=3.8.2 diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf new file mode 100644 index 00000000..15be5f74 --- /dev/null +++ b/modules/nf-core/genmod/score/main.nf @@ -0,0 +1,52 @@ +process GENMOD_SCORE { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0': + 'biocontainers/genmod:3.8.2--pyhdfd78af_0' }" + + input: + tuple val(meta), path(input_vcf) + path (fam) + path (score_config) + + output: + tuple val(meta), path("*_score.vcf"), emit: vcf + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def family_file = fam ? "--family_file ${fam}" : "" + def config_file = score_config ? "--score_config ${score_config}" : "" + """ + genmod \\ + score \\ + $args \\ + $family_file \\ + $config_file \\ + --outfile ${prefix}_score.vcf \\ + $input_vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' ) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}_score.vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/genmod/score/meta.yml b/modules/nf-core/genmod/score/meta.yml new file mode 100644 index 00000000..8998b00c --- /dev/null +++ b/modules/nf-core/genmod/score/meta.yml @@ -0,0 +1,49 @@ +name: "genmod_score" +description: Score the variants of a vcf based on their annotation +keywords: + - score + - ranking + - genmod +tools: + - "genmod": + description: "Annotate genetic inheritance models in variant files" + homepage: "https://github.com/Clinical-Genomics/genmod" + documentation: "https://github.com/Clinical-Genomics/genmod" + tool_dev_url: "https://github.com/moonso" + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_vcf: + type: file + description: vcf file + pattern: "*.{vcf}" + - family_file: + type: file + description: ped file + pattern: "*.{ped}" + - score_config: + type: file + description: rank model config file + pattern: "*.{ini}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - vcf: + type: file + description: Output VCF file + pattern: "*.{vcf}" +authors: + - "@ramprasadn" +maintainers: + - "@ramprasadn" diff --git a/modules/nf-core/genmod/score/tests/main.nf.test b/modules/nf-core/genmod/score/tests/main.nf.test new file mode 100644 index 00000000..d9296fb4 --- /dev/null +++ b/modules/nf-core/genmod/score/tests/main.nf.test @@ -0,0 +1,35 @@ +nextflow_process { + + name "Test Process GENMOD_SCORE" + script "modules/nf-core/genmod/score/main.nf" + process "GENMOD_SCORE" + tag "modules" + tag "modules_nfcore" + tag "genmod" + tag "genmod/score" + + test("genmod_score") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['illumina']['genmod_models_vcf_gz'], checkIfExists: true) + ] + input[1] = file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true) + input[2] = file(params.test_data['homo_sapiens']['illumina']['rank_model'], checkIfExists: true) + """ + } + } + + then { + assertAll( + {assert process.success}, + {assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.2")} + ) + } + + } + +} diff --git a/modules/nf-core/genmod/score/tests/tags.yml b/modules/nf-core/genmod/score/tests/tags.yml new file mode 100644 index 00000000..cef831ed --- /dev/null +++ b/modules/nf-core/genmod/score/tests/tags.yml @@ -0,0 +1,2 @@ +genmod/score: + - modules/nf-core/genmod/score/** diff --git a/modules/nf-core/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml new file mode 100644 index 00000000..361c078b --- /dev/null +++ b/modules/nf-core/tabix/bgzip/environment.yml @@ -0,0 +1,8 @@ +name: tabix_bgzip +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::tabix=1.11 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf new file mode 100644 index 00000000..3065dab0 --- /dev/null +++ b/modules/nf-core/tabix/bgzip/main.nf @@ -0,0 +1,55 @@ +process TABIX_BGZIP { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/htslib:1.19.1--h81da01d_1' : + 'biocontainers/htslib:1.19.1--h81da01d_1' }" + + input: + tuple val(meta), path(input) + + output: + tuple val(meta), path("${output}") , emit: output + tuple val(meta), path("${output}.gzi"), emit: gzi, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + in_bgzip = ["gz", "bgz", "bgzf"].contains(input.getExtension()) + extension = in_bgzip ? input.getBaseName().tokenize(".")[-1] : input.getExtension() + output = in_bgzip ? "${prefix}.${extension}" : "${prefix}.${extension}.gz" + command = in_bgzip ? '-d' : '' + // Name the index according to $prefix, unless a name has been requested + if ((args.matches("(^| )-i\\b") || args.matches("(^| )--index(\$| )")) && !args.matches("(^| )-I\\b") && !args.matches("(^| )--index-name\\b")) { + args = args + " -I ${output}.gzi" + } + """ + bgzip $command -c $args -@${task.cpus} $input > ${output} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS + """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + in_bgzip = ["gz", "bgz", "bgzf"].contains(input.getExtension()) + output = in_bgzip ? input.getBaseName() : "${prefix}.${input.getExtension()}.gz" + + """ + echo "" | gzip > ${output} + touch ${output}.gzi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/tabix/bgzip/meta.yml b/modules/nf-core/tabix/bgzip/meta.yml new file mode 100644 index 00000000..621d49ea --- /dev/null +++ b/modules/nf-core/tabix/bgzip/meta.yml @@ -0,0 +1,52 @@ +name: tabix_bgzip +description: Compresses/decompresses files +keywords: + - compress + - decompress + - bgzip + - tabix +tools: + - bgzip: + description: | + Bgzip compresses or decompresses files in a similar manner to, and compatible with, gzip. + homepage: https://www.htslib.org/doc/tabix.html + documentation: http://www.htslib.org/doc/bgzip.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: file to compress or to decompress +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output: + type: file + description: Output compressed/decompressed file + pattern: "*." + - gzi: + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@joseespinosa" + - "@drpatelh" + - "@maxulysse" + - "@nvnieuwk" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@maxulysse" + - "@nvnieuwk" diff --git a/modules/nf-core/tabix/bgzip/tests/bgzip_compress.config b/modules/nf-core/tabix/bgzip/tests/bgzip_compress.config new file mode 100644 index 00000000..6b6ff55f --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/bgzip_compress.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_BGZIP { + ext.args = ' -i' + } +} diff --git a/modules/nf-core/tabix/bgzip/tests/main.nf.test b/modules/nf-core/tabix/bgzip/tests/main.nf.test new file mode 100644 index 00000000..95fd4c50 --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/main.nf.test @@ -0,0 +1,111 @@ +nextflow_process { + + name "Test Process TABIX_BGZIP" + script "modules/nf-core/tabix/bgzip/main.nf" + process "TABIX_BGZIP" + + tag "modules" + tag "modules_nfcore" + tag "tabix" + tag "tabix/bgzip" + + test("sarscov2_vcf_bgzip_compress") { + when { + process { + """ + input[0] = [ + [ id:'bgzip_test' ], + [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.output[0][1]).name + ).match("bgzip_test") + } + ) + } + } + + test("homo_genome_bedgz_compress") { + when { + process { + """ + input[0] = [ + [ id:'bedgz_test' ], + [ file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.output[0][1]).name + ).match("bedgz_test") + } + ) + } + } + + test("sarscov2_vcf_bgzip_compress_stub") { + options '-stub' + config "./bgzip_compress.config" + + when { + process { + """ + input[0] = [ + [ id:"test_stub" ], + [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.output[0][1]).name + ).match("test_stub") + } + ) + } + } + + test("sarscov2_vcf_bgzip_compress_gzi") { + config "./bgzip_compress.config" + when { + process { + """ + input[0] = [ + [ id:"gzi_compress_test" ], + [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gzi[0][1]).name + ).match("gzi_compress_test") + } + ) + } + } +} diff --git a/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap b/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap new file mode 100644 index 00000000..53d59932 --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap @@ -0,0 +1,186 @@ +{ + "gzi_compress_test": { + "content": [ + "gzi_compress_test.vcf.gz.gzi" + ], + "timestamp": "2024-02-19T14:52:29.328146" + }, + "homo_genome_bedgz_compress": { + "content": [ + { + "0": [ + [ + { + "id": "bedgz_test" + }, + "bedgz_test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,e023292de6ee109a44fc67475d658174" + ], + "gzi": [ + + ], + "output": [ + [ + { + "id": "bedgz_test" + }, + "bedgz_test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,e023292de6ee109a44fc67475d658174" + ] + } + ], + "timestamp": "2024-02-19T14:52:12.422209" + }, + "test_stub": { + "content": [ + "test_stub.vcf.gz" + ], + "timestamp": "2024-02-19T14:52:20.811489" + }, + "sarscov2_vcf_bgzip_compress": { + "content": [ + { + "0": [ + [ + { + "id": "bgzip_test" + }, + "bgzip_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,e023292de6ee109a44fc67475d658174" + ], + "gzi": [ + + ], + "output": [ + [ + { + "id": "bgzip_test" + }, + "bgzip_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "versions": [ + "versions.yml:md5,e023292de6ee109a44fc67475d658174" + ] + } + ], + "timestamp": "2024-02-19T14:52:03.706028" + }, + "sarscov2_vcf_bgzip_compress_gzi": { + "content": [ + { + "0": [ + [ + { + "id": "gzi_compress_test" + }, + "gzi_compress_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "1": [ + [ + { + "id": "gzi_compress_test" + }, + "gzi_compress_test.vcf.gz.gzi:md5,26fd00d4e26141cd11561f6e7d4a2ad0" + ] + ], + "2": [ + "versions.yml:md5,e023292de6ee109a44fc67475d658174" + ], + "gzi": [ + [ + { + "id": "gzi_compress_test" + }, + "gzi_compress_test.vcf.gz.gzi:md5,26fd00d4e26141cd11561f6e7d4a2ad0" + ] + ], + "output": [ + [ + { + "id": "gzi_compress_test" + }, + "gzi_compress_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "versions": [ + "versions.yml:md5,e023292de6ee109a44fc67475d658174" + ] + } + ], + "timestamp": "2024-02-19T14:52:29.271494" + }, + "bgzip_test": { + "content": [ + "bgzip_test.vcf.gz" + ], + "timestamp": "2024-02-19T14:52:03.768295" + }, + "bedgz_test": { + "content": [ + "bedgz_test.bed" + ], + "timestamp": "2024-02-19T14:52:12.453855" + }, + "sarscov2_vcf_bgzip_compress_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test_stub" + }, + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test_stub" + }, + "test_stub.vcf.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e023292de6ee109a44fc67475d658174" + ], + "gzi": [ + [ + { + "id": "test_stub" + }, + "test_stub.vcf.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "output": [ + [ + { + "id": "test_stub" + }, + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,e023292de6ee109a44fc67475d658174" + ] + } + ], + "timestamp": "2024-02-19T14:52:20.769619" + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/bgzip/tests/tags.yml b/modules/nf-core/tabix/bgzip/tests/tags.yml new file mode 100644 index 00000000..de0eec86 --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/tags.yml @@ -0,0 +1,2 @@ +tabix/bgzip: + - "modules/nf-core/tabix/bgzip/**" diff --git a/modules/nf-core/tabix/bgzip/tests/vcf_none.config b/modules/nf-core/tabix/bgzip/tests/vcf_none.config new file mode 100644 index 00000000..f3a3c467 --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/vcf_none.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_BGZIP { + ext.args = '' + } +} diff --git a/nextflow.config b/nextflow.config index c1411fb4..5f30e8dd 100644 --- a/nextflow.config +++ b/nextflow.config @@ -17,7 +17,10 @@ params { tandem_repeats = null trgt_repeats = null variant_catalog = null + reduced_penetrance = null + score_config_snv = null snp_db = null + variant_consequences_snv = null vep_cache = null hificnv_xy = null hificnv_xx = null @@ -287,6 +290,7 @@ manifest { // Load modules.config for DSL2 module specific options includeConfig 'conf/base.config' +includeConfig 'conf/modules/annotate_consequence_pli.config' includeConfig 'conf/modules/annotate_repeat_expansions.config' includeConfig 'conf/modules/general.config' includeConfig 'conf/modules/bam_infer_sex.config' @@ -300,6 +304,7 @@ includeConfig 'conf/modules/phasing.config' includeConfig 'conf/modules/prepare_genome.config' includeConfig 'conf/modules/qc_aligned_reads.config' includeConfig 'conf/modules/scatter_genome.config' +includeConfig 'conf/modules/rank_variants.config' includeConfig 'conf/modules/short_variant_calling.config' includeConfig 'conf/modules/snv_annotation.config' includeConfig 'conf/modules/structural_variant_calling.config' diff --git a/nextflow_schema.json b/nextflow_schema.json index 83ff0550..8f3ae975 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -433,6 +433,12 @@ "format": "file-path", "exists": true }, + "variant_consequences_snv": { + "type": "string", + "description": "File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SNVs.", + "help_text": "For more information check https://ensembl.org/info/genome/variation/prediction/predicted_data.html", + "fa_icon": "fas fa-file-csv" + }, "vep_cache": { "type": "string", "description": "Path to directory of vep_cache", @@ -449,11 +455,13 @@ "hificnv_xy": { "type": "string", "format": "file-path", + "description": "HiFiCNV BED file specifying expected copy number regions for XY samples.", "exists": true }, "hificnv_xx": { "type": "string", "format": "file-path", + "description": "HiFiCNV BED file specifying expected copy number regions for XX samples.", "exists": true }, "hificnv_exclude": { @@ -462,6 +470,20 @@ "description": "HiFiCNV BED file specifying regions to exclude", "exists": true }, + "reduced_penetrance": { + "type": "string", + "exists": true, + "format": "path", + "fa_icon": "fas fa-file-csv", + "description": "File with gene ids that have reduced penetrance. For use with genmod." + }, + "score_config_snv": { + "type": "string", + "exists": true, + "format": "path", + "fa_icon": "fas fa-file", + "description": "SNV rank model config file for genmod." + }, "somalier_sites": { "type": "string", "pattern": "^\\S+\\.vcf(\\.gz)?$", diff --git a/subworkflows/local/annotate_consequence_pli.nf b/subworkflows/local/annotate_consequence_pli.nf new file mode 100644 index 00000000..203a1405 --- /dev/null +++ b/subworkflows/local/annotate_consequence_pli.nf @@ -0,0 +1,30 @@ +// +// A subworkflow to add most severe consequence and pli to a vep annotated vcf +// + +include { ADD_MOST_SEVERE_CSQ } from '../../modules/local/add_most_severe_consequence' +include { ADD_MOST_SEVERE_PLI } from '../../modules/local/add_most_severe_pli' +include { TABIX_BGZIPTABIX } from '../../modules/nf-core/tabix/bgziptabix/main' + +workflow ANNOTATE_CSQ_PLI { + take: + ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] + ch_variant_consequences // channel: [mandatory] [ path(consequences) ] + + main: + ch_versions = Channel.empty() + + ADD_MOST_SEVERE_CSQ (ch_vcf, ch_variant_consequences) + ch_versions = ch_versions.mix(ADD_MOST_SEVERE_CSQ.out.versions) + + ADD_MOST_SEVERE_PLI (ADD_MOST_SEVERE_CSQ.out.vcf) + ch_versions = ch_versions.mix(ADD_MOST_SEVERE_PLI.out.versions) + + TABIX_BGZIPTABIX (ADD_MOST_SEVERE_PLI.out.vcf) + ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions) + + emit: + vcf_ann = TABIX_BGZIPTABIX.out.gz_tbi.map { meta, vcf, tbi -> return [ meta, vcf ] } // channel: [ val(meta), path(vcf) ] + tbi_ann = TABIX_BGZIPTABIX.out.gz_tbi.map { meta, vcf, tbi -> return [ meta, tbi ] } // channel: [ val(meta), path(tbi) ] + versions = ch_versions // channel: [ path(versions.yml) ] +} diff --git a/subworkflows/local/rank_variants/main.nf b/subworkflows/local/rank_variants/main.nf new file mode 100644 index 00000000..c2229ee8 --- /dev/null +++ b/subworkflows/local/rank_variants/main.nf @@ -0,0 +1,51 @@ +// +// A subworkflow to score and rank variants. +// + +include { GENMOD_ANNOTATE } from '../../../modules/nf-core/genmod/annotate/main' +include { GENMOD_MODELS } from '../../../modules/nf-core/genmod/models/main' +include { GENMOD_SCORE } from '../../../modules/nf-core/genmod/score/main' +include { GENMOD_COMPOUND } from '../../../modules/nf-core/genmod/compound/main' +include { BCFTOOLS_SORT } from '../../../modules/nf-core/bcftools/sort/main' +include { TABIX_BGZIP } from '../../../modules/nf-core/tabix/bgzip/main' +include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' + +workflow RANK_VARIANTS { + + take: + ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] + ch_pedfile // channel: [mandatory] [ path(ped) ] + ch_reduced_penetrance // channel: [mandatory] [ path(pentrance) ] + ch_score_config // channel: [mandatory] [ path(ini) ] + + main: + ch_versions = Channel.empty() + + GENMOD_ANNOTATE(ch_vcf) + + GENMOD_MODELS(GENMOD_ANNOTATE.out.vcf, ch_pedfile, ch_reduced_penetrance) + + GENMOD_SCORE(GENMOD_MODELS.out.vcf, ch_pedfile, ch_score_config) + + GENMOD_COMPOUND(GENMOD_SCORE.out.vcf) + + BCFTOOLS_SORT(GENMOD_COMPOUND.out.vcf) // SV file needs to be sorted before indexing + + TABIX_BGZIP(GENMOD_COMPOUND.out.vcf) //run only for SNVs + + ch_vcf = TABIX_BGZIP.out.output.mix(BCFTOOLS_SORT.out.vcf) + + TABIX_TABIX (ch_vcf) + + ch_versions = ch_versions.mix(GENMOD_ANNOTATE.out.versions) + ch_versions = ch_versions.mix(GENMOD_MODELS.out.versions) + ch_versions = ch_versions.mix(GENMOD_SCORE.out.versions) + ch_versions = ch_versions.mix(GENMOD_COMPOUND.out.versions) + ch_versions = ch_versions.mix(BCFTOOLS_SORT.out.versions) + ch_versions = ch_versions.mix(TABIX_BGZIP.out.versions) + ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) + + emit: + vcf = ch_vcf // channel: [ val(meta), path(vcf) ] + versions = ch_versions // channel: [ path(versions.yml) ] +} diff --git a/subworkflows/local/short_variant_calling/main.nf b/subworkflows/local/short_variant_calling/main.nf index 7470314d..8bdaf9f5 100644 --- a/subworkflows/local/short_variant_calling/main.nf +++ b/subworkflows/local/short_variant_calling/main.nf @@ -63,8 +63,17 @@ workflow SHORT_VARIANT_CALLING { // Multisample BCFTOOLS_SORT_GVCF.out.vcf - .map { meta, gvcf -> [ ['id':'multisample'], gvcf ] } - .groupTuple() + .map { meta, gvcf -> [ 'multisample', meta.phenotype == 2, gvcf ] } + .groupTuple() // Group all files together + // If any of the samples in the VCF have an affected phenotype (2) + // add this to the meta of the multisample VCF to know if we should run RANK_VARIANTS or not + .map { id, affected, gvcfs -> + new_meta = [ + 'id': id, + 'contains_affected': affected.any(), + ] + [ new_meta, gvcfs ] + } .set{ glnexus_in } GLNEXUS( glnexus_in, ch_bed ) diff --git a/subworkflows/local/short_variant_calling/tests/main.nf.test.snap b/subworkflows/local/short_variant_calling/tests/main.nf.test.snap index 41275cac..e0400854 100644 --- a/subworkflows/local/short_variant_calling/tests/main.nf.test.snap +++ b/subworkflows/local/short_variant_calling/tests/main.nf.test.snap @@ -14,7 +14,8 @@ "1": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,e6dd7f56772c154750e937d9a56baa6d" ] @@ -33,7 +34,8 @@ "combined_bcf": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,e6dd7f56772c154750e937d9a56baa6d" ] @@ -64,7 +66,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-09T11:59:06.873173703" + "timestamp": "2024-07-17T15:31:23.096622148" }, "2 samples - 2 bed, fasta, fai, bed": { "content": [ @@ -88,7 +90,8 @@ "1": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,7533ee89ae115f8f78ac26d29efc78d3" ] @@ -115,7 +118,8 @@ "combined_bcf": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,7533ee89ae115f8f78ac26d29efc78d3" ] @@ -161,7 +165,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-09T12:00:06.733280923" + "timestamp": "2024-07-17T15:32:23.136568046" }, "2 samples - 2 bed, fasta, fai, bed - stub": { "content": [ @@ -185,7 +189,8 @@ "1": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] @@ -212,7 +217,8 @@ "combined_bcf": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] @@ -258,7 +264,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-09T12:01:17.865011558" + "timestamp": "2024-07-17T15:33:33.799209289" }, "1 sample - no bed, fasta, fai, []": { "content": [ @@ -275,7 +281,8 @@ "1": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,e6dd7f56772c154750e937d9a56baa6d" ] @@ -294,7 +301,8 @@ "combined_bcf": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,e6dd7f56772c154750e937d9a56baa6d" ] @@ -325,7 +333,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-09T11:58:11.914343709" + "timestamp": "2024-07-17T15:30:27.757141768" }, "1 sample - 1 bed, fasta, fai, []": { "content": [ @@ -342,7 +350,8 @@ "1": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,e6dd7f56772c154750e937d9a56baa6d" ] @@ -361,7 +370,8 @@ "combined_bcf": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,e6dd7f56772c154750e937d9a56baa6d" ] @@ -392,7 +402,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-09T11:58:39.573530566" + "timestamp": "2024-07-17T15:30:55.576093313" }, "1 sample - 1 bed, fasta, fai, [] - stub": { "content": [ @@ -409,7 +419,8 @@ "1": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] @@ -428,7 +439,8 @@ "combined_bcf": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] @@ -459,7 +471,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-09T12:00:33.980507128" + "timestamp": "2024-07-17T15:32:50.513361746" }, "1 sample - 1 bed, fasta, fai, bed - stub": { "content": [ @@ -476,7 +488,8 @@ "1": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] @@ -495,7 +508,8 @@ "combined_bcf": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] @@ -526,7 +540,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-09T12:00:47.655880789" + "timestamp": "2024-07-17T15:33:04.262079116" }, "1 sample - no bed, fasta, fai, [] - stub": { "content": [ @@ -543,7 +557,8 @@ "1": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] @@ -562,7 +577,8 @@ "combined_bcf": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] @@ -593,7 +609,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-09T12:00:20.154541832" + "timestamp": "2024-07-17T15:32:36.6951779" }, "1 sample - 2 bed, fasta, fai, bed": { "content": [ @@ -610,7 +626,8 @@ "1": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,e6dd7f56772c154750e937d9a56baa6d" ] @@ -630,7 +647,8 @@ "combined_bcf": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,e6dd7f56772c154750e937d9a56baa6d" ] @@ -662,7 +680,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-09T11:59:35.482195945" + "timestamp": "2024-07-17T15:31:51.744004194" }, "1 sample - 2 bed, fasta, fai, bed - stub": { "content": [ @@ -679,7 +697,8 @@ "1": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] @@ -699,7 +718,8 @@ "combined_bcf": [ [ { - "id": "multisample" + "id": "multisample", + "contains_affected": false }, "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] @@ -731,6 +751,6 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-09T12:01:02.557411667" + "timestamp": "2024-07-17T15:33:18.116317115" } } \ No newline at end of file diff --git a/subworkflows/local/snv_annotation/tests/main.nf.test.snap b/subworkflows/local/snv_annotation/tests/main.nf.test.snap deleted file mode 100644 index 8c915b21..00000000 --- a/subworkflows/local/snv_annotation/tests/main.nf.test.snap +++ /dev/null @@ -1,164 +0,0 @@ -{ - "bcf, db, vep_cache, '110'": { - "content": [ - [ - "versions.yml:md5,797275193dd19766e99030e63c23bd5f", - "versions.yml:md5,89437847140da33e3bfb17867507f30d", - "versions.yml:md5,a07924ee4ebc2d4de5bb7ef897ddc30c", - "versions.yml:md5,c0e55e36a31ed71acf25702b7d059533" - ], - "multisample.vcf.gz.tbi", - [ - "##INFO=", - "##VEP-command-line='vep --assembly GRCh38 --cache --cache_version 110 --compress_output bgzip --database 0 --dir_cache [PATH]/vep_cache --fasta hg38.test.fa --fork 2 --input_file multisample.bcf.gz_filltags.vcf --offline --output_file multisample.vcf.gz --vcf'", - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tdefault", - "chr16\t63972\tchr16_63972_T_C\tT\tC\t45\t.\tAF=1;AQ=45;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000262316|protein_coding||3/17||||||||||-1||HGNC|HGNC:20561,C|intron_variant&NMD_transcript_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000417043|nonsense_mediated_decay||2/3||||||||||-1||HGNC|HGNC:20561,C|intron_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000419764|protein_coding||3/3||||||||||-1|cds_end_NF|HGNC|HGNC:20561,C|intron_variant&NMD_transcript_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000428730|nonsense_mediated_decay||2/16||||||||||-1||HGNC|HGNC:20561,C|upstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000448893|protein_coding|||||||||||4210|-1|cds_start_NF|HGNC|HGNC:20561,C|intron_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000450643|protein_coding||3/4||||||||||-1|cds_end_NF|HGNC|HGNC:20561,C|downstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000472390|retained_intron|||||||||||580|-1||HGNC|HGNC:20561,C|upstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000482904|retained_intron|||||||||||1766|-1||HGNC|HGNC:20561,C|upstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000486045|retained_intron|||||||||||3779|-1||HGNC|HGNC:20561,C|non_coding_transcript_exon_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000487201|retained_intron|2/3||||1177|||||||-1||HGNC|HGNC:20561,C|upstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000493647|retained_intron|||||||||||3292|-1||HGNC|HGNC:20561\tGT:DP:AD:GQ:PL:RNC\t1/1:13:0,13:32:45,32,0:..", - "chr16\t86889\tchr16_86889_T_C\tT\tC\t68\t.\tAF=1;AQ=68;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|downstream_gene_variant|MODIFIER|MPG|ENSG00000103152|Transcript|ENST00000219431|protein_coding|||||||||||1047|1||HGNC|HGNC:7211,C|downstream_gene_variant|MODIFIER|MPG|ENSG00000103152|Transcript|ENST00000356432|protein_coding|||||||||||1043|1||HGNC|HGNC:7211,C|downstream_gene_variant|MODIFIER|MPG|ENSG00000103152|Transcript|ENST00000397817|protein_coding|||||||||||1038|1||HGNC|HGNC:7211,C|intron_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000399953|protein_coding||11/11||||||||||-1||HGNC|HGNC:14124,C|downstream_gene_variant|MODIFIER|MPG|ENSG00000103152|Transcript|ENST00000436333|protein_coding|||||||||||1205|1|cds_end_NF|HGNC|HGNC:7211,C|upstream_gene_variant|MODIFIER||ENSG00000269482|Transcript|ENST00000601483|lncRNA|||||||||||3742|1|||,C|intron_variant&non_coding_transcript_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000610509|retained_intron||1/2||||||||||-1||HGNC|HGNC:14124,C|intron_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000611875|protein_coding||13/13||||||||||-1||HGNC|HGNC:14124,C|intron_variant&NMD_transcript_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000621703|nonsense_mediated_decay||10/10||||||||||-1||HGNC|HGNC:14124,C|intron_variant&NMD_transcript_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000622194|nonsense_mediated_decay||11/11||||||||||-1||HGNC|HGNC:14124\tGT:DP:AD:GQ:PL:RNC\t1/1:28:0,28:65:68,67,0:..", - "chr16\t160055\tchr16_160055_C_G\tC\tG\t58\t.\tAF=1;AQ=58;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3067|1||HGNC|HGNC:4836,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4427|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:30:0,29:51:58,51,0:..", - "chr16\t160070\tchr16_160070_C_CGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT\tC\tCGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT\t0\t.\tAF=0.5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3051|1||HGNC|HGNC:4836,GGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4411|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:30:8,7:3:19,0,14:..", - "chr16\t160089\tchr16_160089_TG_T\tTG\tT\t4\t.\tAF=0.5;AQ=4;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3032|1||HGNC|HGNC:4836,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4392|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:30:25,5:6:4,0,29:..", - "chr16\t160180\tchr16_160180_C_T\tC\tT\t48\t.\tAF=1;AQ=48;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2942|1||HGNC|HGNC:4836,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4302|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:29:1,28:36:48,36,0:..", - "chr16\t160216\tchr16_160216_T_A\tT\tA\t48\t.\tAF=1;AQ=48;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2906|1||HGNC|HGNC:4836,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4266|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:30:0,27:41:48,41,0:..", - "chr16\t160217\tchr16_160217_C_T\tC\tT\t55\t.\tAF=1;AQ=55;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2905|1||HGNC|HGNC:4836,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4265|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:27:0,27:40:55,40,0:..", - "chr16\t160326\tchr16_160326_T_A\tT\tA\t56\t.\tAF=1;AQ=56;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2796|1||HGNC|HGNC:4836,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4156|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:30:0,29:53:56,55,0:..", - "chr16\t160327\tchr16_160327_C_T\tC\tT\t41\t.\tAF=1;AQ=41;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2795|1||HGNC|HGNC:4836,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4155|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:29:3,26:22:41,22,0:..", - "chr16\t160388\tchr16_160388_G_GGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA\tG\tGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA\t31\t.\tAF=1;AQ=31;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=GGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2733|1||HGNC|HGNC:4836,GGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4093|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:31:4,14:15:31,14,0:..", - "chr16\t160728\tchr16_160728_C_T\tC\tT\t31\t.\tAF=1;AQ=31;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2394|1||HGNC|HGNC:4836,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3754|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:30:8,22:8:31,7,0:..", - "chr16\t160746\tchr16_160746_T_C\tT\tC\t1\t.\tAF=0.5;AQ=1;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2376|1||HGNC|HGNC:4836,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3736|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:30:23,7:4:1,0,33:..", - "chr16\t160751\tchr16_160752_G_GGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA;chr16_160751_AG_A\tAG\tA\t19\t.\tAF=0.5;AQ=0;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2370|1||HGNC|HGNC:4836,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3730|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:22:.,7:4:0,0,0:..", - "chr16\t160752\tchr16_160752_G_GGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA;chr16_160751_AG_A\tG\tGGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA\t19\t.\tAF=0.5;AQ=19;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2369|1||HGNC|HGNC:4836,GGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3729|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/0:22:.,14:4:0,0,0:..", - "chr16\t162329\tchr16_162329_G_A\tG\tA\t53\t.\tAF=0.5;AQ=53;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||793|1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||3649|1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||2153|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:53:53,0,70:..", - "chr16\t162650\tchr16_162650_C_T\tC\tT\t57\t.\tAF=0.5;AQ=57;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||472|1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||3328|1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1832|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:24:9,15:57:57,0,66:..", - "chr16\t163106\tchr16_163106_C_T\tC\tT\t49\t.\tAF=0.5;AQ=49;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||16|1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2872|1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1376|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:50:49,0,68:..", - "chr16\t163140\tchr16_163140_T_G\tT\tG\t43\t.\tAF=0.5;AQ=43;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|non_coding_transcript_exon_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|1/3||||19|||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2838|1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1342|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:43:43,0,61:..", - "chr16\t163143\tchr16_163143_G_A\tG\tA\t43\t.\tAF=0.5;AQ=43;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|non_coding_transcript_exon_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|1/3||||22|||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2835|1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1339|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:44:43,0,62:..", - "chr16\t163229\tchr16_163229_T_C\tT\tC\t28\t.\tAF=0.5;AQ=28;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2749|1||HGNC|HGNC:4826,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1253|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:29:28,0,54:..", - "chr16\t163287\tchr16_163287_C_G\tC\tG\t4\t.\tAF=0.5;AQ=4;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2691|1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1195|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:6:4,0,35:..", - "chr16\t163292\tchr16_163292_A_G\tA\tG\t6\t.\tAF=0.5;AQ=6;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2686|1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1190|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:7:6,0,37:..", - "chr16\t163432\tchr16_163432_AGTGGGGAGGGGACAGTGAGGAGGGGACC_A\tAGTGGGGAGGGGACAGTGAGGAGGGGACC\tA\t18\t.\tAF=0.5;AQ=18;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2518|1||HGNC|HGNC:4826,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1022|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:19:4,10:4:18,0,2:..", - "chr16\t163499\tchr16_163499_G_C\tG\tC\t11\t.\tAF=0.5;AQ=11;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2479|1||HGNC|HGNC:4826,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||983|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:19:12,7:12:11,0,35:..", - "chr16\t163513\tchr16_163513_G_C\tG\tC\t5\t.\tAF=0.5;AQ=5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2465|1||HGNC|HGNC:4826,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||969|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:14,7:6:5,0,32:..", - "chr16\t163519\tchr16_163519_A_G\tA\tG\t9\t.\tAF=0.5;AQ=9;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2459|1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||963|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:22:15,7:10:9,0,39:..", - "chr16\t163796\tchr16_163796_T_A\tT\tA\t15\t.\tAF=0.5;AQ=15;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2182|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4883|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||686|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:15:0,15:5:15,0,3:..", - "chr16\t163800\tchr16_163800_G_A\tG\tA\t17\t.\tAF=0.5;AQ=17;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2178|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4879|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||682|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:16:2,14:4:17,0,1:..", - "chr16\t163804\tchr16_163804_G_A\tG\tA\t25\t.\tAF=1;AQ=25;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2174|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4875|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||678|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:0,21:22:25,24,0:..", - "chr16\t164431\tchr16_164431_T_TG\tT\tTG\t58\t.\tAF=1;AQ=58;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1546|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4247|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||50|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:0,21:48:58,48,0:..", - "chr16\t164541\tchr16_164541_G_GGTCC\tG\tGGTCC\t52\t.\tAF=0.5;AQ=52;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GTCC|non_coding_transcript_exon_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|2/3||||155-156|||||||1||HGNC|HGNC:4836,GTCC|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1436|1||HGNC|HGNC:4826,GTCC|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4137|1||HGNC|HGNC:4825,GTCC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GTCC|non_coding_transcript_exon_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|1/3||||60-61|||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:13,7:52:52,0,62:..", - "chr16\t164690\tchr16_164690_C_CGCGGGGCGCGGTGCGGGCGGG\tC\tCGCGGGGCGCGGTGCGGGCGGG\t22\t.\tAF=1;AQ=22;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=GCGGGGCGCGGTGCGGGCGGG|splice_donor_region_variant&intron_variant&non_coding_transcript_variant|LOW|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GCGGGGCGCGGTGCGGGCGGG|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1287|1||HGNC|HGNC:4826,GCGGGGCGCGGTGCGGGCGGG|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3988|1||HGNC|HGNC:4825,GCGGGGCGCGGTGCGGGCGGG|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GCGGGGCGCGGTGCGGGCGGG|splice_donor_region_variant&intron_variant&non_coding_transcript_variant|LOW|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:6,14:7:22,6,0:..", - "chr16\t164723\tchr16_164723_C_T\tC\tT\t20\t.\tAF=0.5;AQ=20;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1255|1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3956|1||HGNC|HGNC:4825,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:15,4:21:20,0,40:..", - "chr16\t164731\tchr16_164731_C_CG;chr16_164731_C_CGGGGTCGCG\tC\tCG\t16\t.\tAF=0.5;AQ=16;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1246|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3947|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/0:21:2,14:10:22,16,13:..", - "chr16\t164731\tchr16_164731_C_CG;chr16_164731_C_CGGGGTCGCG\tC\tCGGGGTCGCG\t16\t.\tAF=0.5;AQ=13;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GGGGTCGCG|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GGGGTCGCG|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1246|1||HGNC|HGNC:4826,GGGGTCGCG|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3947|1||HGNC|HGNC:4825,GGGGTCGCG|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GGGGTCGCG|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:2,4:10:22,16,28:..", - "chr16\t164740\tchr16_164740_C_T\tC\tT\t47\t.\tAF=1;AQ=47;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1238|1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3939|1||HGNC|HGNC:4825,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:20:1,18:42:47,43,0:..", - "chr16\t164771\tchr16_164771_T_C\tT\tC\t22\t.\tAF=0.5;AQ=22;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1207|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3908|1||HGNC|HGNC:4825,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:13,6:23:22,0,41:..", - "chr16\t164791\tchr16_164791_G_A\tG\tA\t39\t.\tAF=0.5;AQ=39;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1187|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3888|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:6,15:20:39,0,19:..", - "chr16\t164800\tchr16_164800_G_GGCGGGGTCGCGGGGCGGGGCGAGGTC\tG\tGGCGGGGTCGCGGGGCGGGGCGAGGTC\t16\t.\tAF=0.5;AQ=16;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GCGGGGTCGCGGGGCGGGGCGAGGTC|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GCGGGGTCGCGGGGCGGGGCGAGGTC|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1177|1||HGNC|HGNC:4826,GCGGGGTCGCGGGGCGGGGCGAGGTC|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3878|1||HGNC|HGNC:4825,GCGGGGTCGCGGGGCGGGGCGAGGTC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GCGGGGTCGCGGGGCGGGGCGAGGTC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:14,4:17:16,0,39:..", - "chr16\t164817\tchr16_164817_C_A\tC\tA\t41\t.\tAF=0.5;AQ=41;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1161|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3862|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:8,13:30:41,0,30:..", - "chr16\t164831\tchr16_164831_C_CG\tC\tCG\t15\t.\tAF=1;AQ=15;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1146|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3847|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:4,15:3:15,0,0:..", - "chr16\t164839\tchr16_164839_G_GGT\tG\tGGT\t15\t.\tAF=1;AQ=15;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=GT|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GT|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1138|1||HGNC|HGNC:4826,GT|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3839|1||HGNC|HGNC:4825,GT|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GT|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:2,15:4:15,1,0:..", - "chr16\t164871\tchr16_164871_T_G\tT\tG\t39\t.\tAF=0.5;AQ=39;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1107|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3808|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:20:12,7:39:39,0,51:..", - "chr16\t164884\tchr16_164884_G_GT\tG\tGT\t51\t.\tAF=1;AQ=51;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1093|1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3794|1||HGNC|HGNC:4825,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:0,21:50:51,53,0:..", - "chr16\t164907\tchr16_164907_C_A\tC\tA\t43\t.\tAF=0.5;AQ=43;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1071|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3772|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:20:12,8:43:43,0,60:..", - "chr16\t164930\tchr16_164930_T_C\tT\tC\t0\t.\tAF=0.5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1048|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3749|1||HGNC|HGNC:4825,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:1,8:14:5,0,71:..", - "chr16\t164931\tchr16_164931_C_G\tC\tG\t24\t.\tAF=0.5;AQ=24;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1047|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3748|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t./1:9:.,8:.:0,0,0:O.", - "chr16\t164932\tchr16_164932_G_GGGCGGGC\tG\tGGGCGGGC\t12\t.\tAF=0.5;AQ=12;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GGCGGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GGCGGGC|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1045|1||HGNC|HGNC:4826,GGCGGGC|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3746|1||HGNC|HGNC:4825,GGCGGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GGCGGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t./1:9:.,7:.:0,0,0:O.", - "chr16\t164942\tchr16_164942_G_GT\tG\tGT\t22\t.\tAF=0.5;AQ=22;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1035|1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3736|1||HGNC|HGNC:4825,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t./1:9:.,8:.:0,0,0:O.", - "chr16\t164953\tchr16_164953_G_GGCGGC\tG\tGGCGGC\t31\t.\tAF=0.5;AQ=31;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GCGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GCGGC|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1024|1||HGNC|HGNC:4826,GCGGC|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3725|1||HGNC|HGNC:4825,GCGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GCGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:14,6:32:31,0,43:..", - "chr16\t164985\tchr16_164985_C_CG\tC\tCG\t54\t.\tAF=1;AQ=54;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||992|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3693|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:19:1,18:50:54,52,0:..", - "chr16\t165380\tchr16_165380_G_A\tG\tA\t48\t.\tAF=0.5;AQ=48;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||224|1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||598|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3299|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:22:14,8:48:48,0,68:..", - "chr16\t165856\tchr16_165856_G_C\tG\tC\t46\t.\tAF=0.5;AQ=46;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||700|1||HGNC|HGNC:4836,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||122|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2823|1||HGNC|HGNC:4825,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:22:14,8:47:46,0,64:..", - "chr16\t166191\tchr16_166191_C_CG\tC\tCG\t45\t.\tAF=0.5;AQ=45;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||1035|1||HGNC|HGNC:4836,G|intron_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2487|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:22:14,6:45:45,0,56:..", - "chr16\t167947\tchr16_167947_T_TC\tT\tTC\t29\t.\tAF=1;AQ=29;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||4928|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2791|1||HGNC|HGNC:4836,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1183|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||4942|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||731|1||HGNC|HGNC:4825,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||1186|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||4946|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||4996|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1186|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:11,10:14:29,14,0:..", - "chr16\t168533\tchr16_168533_T_C\tT\tC\t55\t.\tAF=0.5;AQ=55;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||4343|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3377|1||HGNC|HGNC:4836,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1769|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||4357|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||146|1||HGNC|HGNC:4825,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||1772|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||4361|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||4411|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1772|1||HGNC|HGNC:4826,C|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||4969|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:11,9:56:55,0,69:..", - "chr16\t168736\tchr16_168736_A_G\tA\tG\t52\t.\tAF=0.5;AQ=52;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||4140|1||HGNC|HGNC:4824,G|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3580|1||HGNC|HGNC:4836,G|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1972|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||4154|1||HGNC|HGNC:4824,G|non_coding_transcript_exon_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|1/3||||58|||||||1||HGNC|HGNC:4825,G|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||1975|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||4158|1||HGNC|HGNC:4824,G|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||4208|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,G|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1975|1||HGNC|HGNC:4826,G|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||4766|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:11,9:52:52,0,64:..", - "chr16\t170831\tchr16_170831_T_TCACA;chr16_170831_T_TCACACA\tT\tTCACA\t20\t.\tAF=0.5;AQ=20;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=CACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||2044|1||HGNC|HGNC:4824,CACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4067|1||HGNC|HGNC:4826,CACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||2058|1||HGNC|HGNC:4824,CACA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1497|1||HGNC|HGNC:4825,CACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4070|1||HGNC|HGNC:4826,CACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||2062|1||HGNC|HGNC:4824,CACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||2112|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,CACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4070|1||HGNC|HGNC:4826,CACA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2670|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/0:20:6,6:17:38,20,33:..", - "chr16\t170831\tchr16_170831_T_TCACA;chr16_170831_T_TCACACA\tT\tTCACACA\t20\t.\tAF=0.5;AQ=20;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=CACACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||2044|1||HGNC|HGNC:4824,CACACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4067|1||HGNC|HGNC:4826,CACACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||2058|1||HGNC|HGNC:4824,CACACA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1497|1||HGNC|HGNC:4825,CACACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4070|1||HGNC|HGNC:4826,CACACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||2062|1||HGNC|HGNC:4824,CACACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||2112|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,CACACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4070|1||HGNC|HGNC:4826,CACACA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2670|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:6,5:17:38,20,35:..", - "chr16\t171206\tchr16_171206_T_TTTA\tT\tTTTA\t5\t.\tAF=1;AQ=5;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=TTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1669|1||HGNC|HGNC:4824,TTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4442|1||HGNC|HGNC:4826,TTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1683|1||HGNC|HGNC:4824,TTA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1872|1||HGNC|HGNC:4825,TTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4445|1||HGNC|HGNC:4826,TTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1687|1||HGNC|HGNC:4824,TTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1737|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,TTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4445|1||HGNC|HGNC:4826,TTA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2295|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:20:11,9:3:5,1,0:..", - "chr16\t171220\tchr16_171220_T_TATTA\tT\tTATTA\t4\t.\tAF=0.5;AQ=4;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1655|1||HGNC|HGNC:4824,ATTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4456|1||HGNC|HGNC:4826,ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1669|1||HGNC|HGNC:4824,ATTA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1886|1||HGNC|HGNC:4825,ATTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4459|1||HGNC|HGNC:4826,ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1673|1||HGNC|HGNC:4824,ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1723|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,ATTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4459|1||HGNC|HGNC:4826,ATTA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2281|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:16,4:6:4,0,27:..", - "chr16\t172417\tchr16_172417_C_T\tC\tT\t56\t.\tAF=1;AQ=56;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||459|1||HGNC|HGNC:4824,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4263|1||HGNC|HGNC:4823,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4287|1||HGNC|HGNC:4823,T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||473|1||HGNC|HGNC:4824,T|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3083|1||HGNC|HGNC:4825,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4281|1||HGNC|HGNC:4823,T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||477|1||HGNC|HGNC:4824,T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||527|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4331|1||HGNC|HGNC:4823,T|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4896|-1|||,T|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1085|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:19:0,19:53:56,55,0:..", - "chr16\t172418\tchr16_172418_T_C\tT\tC\t57\t.\tAF=1;AQ=57;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||458|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4262|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4286|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||472|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3084|1||HGNC|HGNC:4825,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4280|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||476|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||526|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4330|1||HGNC|HGNC:4823,C|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4895|-1|||,C|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1084|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:18:0,18:54:57,57,0:..", - "chr16\t172636\tchr16_172636_C_T\tC\tT\t64\t.\tAF=1;AQ=64;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||240|1||HGNC|HGNC:4824,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4044|1||HGNC|HGNC:4823,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4068|1||HGNC|HGNC:4823,T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||254|1||HGNC|HGNC:4824,T|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3302|1||HGNC|HGNC:4825,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4062|1||HGNC|HGNC:4823,T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||258|1||HGNC|HGNC:4824,T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||308|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4112|1||HGNC|HGNC:4823,T|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4677|-1|||,T|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||866|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:18:1,17:59:64,60,0:..", - "chr16\t172870\tchr16_172870_G_C\tG\tC\t63\t.\tAF=1;AQ=63;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||6|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||3810|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||3834|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||20|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3536|1||HGNC|HGNC:4825,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||3828|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||24|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||74|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||3878|1||HGNC|HGNC:4823,C|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4443|-1|||,C|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||632|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:18:0,18:58:63,59,0:..", - "chr16\t173707\tchr16_173707_A_G\tA\tG\t66\t.\tAF=1;AQ=66;AC=2;cadd_raw=0.19;cadd_phred=3.05;CSQ=G|3_prime_UTR_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|3/3||||573|||||||1||HGNC|HGNC:4824,G|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||2973|1||HGNC|HGNC:4823,G|upstream_gene_variant|MODIFIER|Y_RNA|ENSG00000207243|Transcript|ENST00000384514|misc_RNA|||||||||||4847|1||RFAM|,G|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||2997|1||HGNC|HGNC:4823,G|3_prime_UTR_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|3/3||||510|||||||1||HGNC|HGNC:4824,G|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4373|1||HGNC|HGNC:4825,G|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||2991|1||HGNC|HGNC:4823,G|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||32|1||HGNC|HGNC:4824,G|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||244|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,G|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||3041|1||HGNC|HGNC:4823,G|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||3606|-1|||,G|upstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||47|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:19:0,19:63:66,65,0:..", - "chr16\t274052\tchr16_274052_A_G\tA\tG\t66\t.\tAF=1;AQ=66;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|synonymous_variant&NMD_transcript_variant|LOW|RGS11|ENSG00000076344|Transcript|ENST00000168869|nonsense_mediated_decay|5/15||||353|250|84|L|Tta/Cta|||-1||HGNC|HGNC:9993,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000301679|protein_coding|||||||||||3972|1||HGNC|HGNC:14163,G|synonymous_variant|LOW|RGS11|ENSG00000076344|Transcript|ENST00000316163|protein_coding|6/17||||434|357|119|D|gaT/gaC|||-1||HGNC|HGNC:9993,G|synonymous_variant|LOW|RGS11|ENSG00000076344|Transcript|ENST00000359740|protein_coding|5/16||||387|387|129|D|gaT/gaC|||-1||HGNC|HGNC:9993,G|synonymous_variant|LOW|RGS11|ENSG00000076344|Transcript|ENST00000397770|protein_coding|6/17||||453|420|140|D|gaT/gaC|||-1||HGNC|HGNC:9993,G|downstream_gene_variant|MODIFIER|RGS11|ENSG00000076344|Transcript|ENST00000472466|retained_intron|||||||||||887|-1||HGNC|HGNC:9993,G|non_coding_transcript_exon_variant|MODIFIER|RGS11|ENSG00000076344|Transcript|ENST00000477143|retained_intron|1/9||||905|||||||-1||HGNC|HGNC:9993,G|non_coding_transcript_exon_variant|MODIFIER|RGS11|ENSG00000076344|Transcript|ENST00000481672|retained_intron|2/11||||110|||||||-1||HGNC|HGNC:9993,G|non_coding_transcript_exon_variant|MODIFIER|RGS11|ENSG00000076344|Transcript|ENST00000493449|retained_intron|5/9||||1199|||||||-1||HGNC|HGNC:9993,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000600536|nonsense_mediated_decay|||||||||||4109|1||HGNC|HGNC:14163,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000653392|nonsense_mediated_decay|||||||||||4216|1||HGNC|HGNC:14163,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000654053|nonsense_mediated_decay|||||||||||4154|1||HGNC|HGNC:14163,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000659283|nonsense_mediated_decay|||||||||||1869|1||HGNC|HGNC:14163,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000666018|nonsense_mediated_decay|||||||||||4097|1||HGNC|HGNC:14163\tGT:DP:AD:GQ:PL:RNC\t1/1:32:0,32:64:66,66,0:..", - "chr16\t286660\tchr16_286660_G_A\tG\tA\t65\t.\tAF=1;AQ=65;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|synonymous_variant|LOW|PDIA2|ENSG00000185615|Transcript|ENST00000219406|protein_coding|9/11||||1353|1347|449|T|acG/acA|||1||HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|ARHGDIG|ENSG00000242173|Transcript|ENST00000219409|protein_coding|||||||||||3650|1||HGNC|HGNC:680,A|downstream_gene_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000262320|protein_coding|||||||||||780|-1||HGNC|HGNC:903,A|downstream_gene_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000354866|protein_coding|||||||||||781|-1||HGNC|HGNC:903,A|synonymous_variant|LOW|PDIA2|ENSG00000185615|Transcript|ENST00000404312|protein_coding|9/11||||1343|1338|446|T|acG/acA|||1||HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|ARHGDIG|ENSG00000242173|Transcript|ENST00000414650|protein_coding|||||||||||3850|1|cds_end_NF|HGNC|HGNC:680,A|synonymous_variant|LOW|PDIA2|ENSG00000185615|Transcript|ENST00000435833|protein_coding|3/5||||234|234|78|T|acG/acA|||1|cds_start_NF|HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|ARHGDIG|ENSG00000242173|Transcript|ENST00000447871|protein_coding|||||||||||3972|1|cds_end_NF|HGNC|HGNC:680,A|downstream_gene_variant|MODIFIER|PDIA2|ENSG00000185615|Transcript|ENST00000456379|protein_coding|||||||||||1520|1|cds_start_NF&cds_end_NF|HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000457798|protein_coding|||||||||||1530|-1|cds_start_NF|HGNC|HGNC:903,A|downstream_gene_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000461023|retained_intron|||||||||||780|-1||HGNC|HGNC:903,A|downstream_gene_variant|MODIFIER|PDIA2|ENSG00000185615|Transcript|ENST00000462950|protein_coding_CDS_not_defined|||||||||||1084|1||HGNC|HGNC:14180,A|non_coding_transcript_exon_variant|MODIFIER|PDIA2|ENSG00000185615|Transcript|ENST00000467212|retained_intron|8/10||||1418|||||||1||HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|ARHGDIG|ENSG00000242173|Transcript|ENST00000477621|retained_intron|||||||||||3820|1||HGNC|HGNC:680,A|non_coding_transcript_exon_variant|MODIFIER|PDIA2|ENSG00000185615|Transcript|ENST00000482665|retained_intron|5/7||||1630|||||||1||HGNC|HGNC:14180\tGT:DP:AD:GQ:PL:RNC\t1/1:22:0,22:60:65,61,0:..", - "chr16\t309953\tchr16_309953_A_G\tA\tG\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000262320|protein_coding||4/10||||||||||-1||HGNC|HGNC:903,G|intron_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000354866|protein_coding||4/9||||||||||-1||HGNC|HGNC:903,G|intron_variant&non_coding_transcript_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000461023|retained_intron||3/7||||||||||-1||HGNC|HGNC:903,G|intron_variant&non_coding_transcript_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000481769|protein_coding_CDS_not_defined||3/4||||||||||-1||HGNC|HGNC:903\tGT:DP:AD:GQ:PL:RNC\t0/1:11:6,5:34:34,0,51:..", - "chr16\t346264\tchr16_346264_A_G\tA\tG\t30\t.\tAF=0.5;AQ=30;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|synonymous_variant|LOW|AXIN1|ENSG00000103126|Transcript|ENST00000262320|protein_coding|2/11||||1198|762|254|D|gaT/gaC|||-1||HGNC|HGNC:903,G|synonymous_variant|LOW|AXIN1|ENSG00000103126|Transcript|ENST00000354866|protein_coding|2/10||||924|762|254|D|gaT/gaC|||-1||HGNC|HGNC:903,G|non_coding_transcript_exon_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000461023|retained_intron|1/8||||59|||||||-1||HGNC|HGNC:903,G|intron_variant&non_coding_transcript_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000481769|protein_coding_CDS_not_defined||1/4||||||||||-1||HGNC|HGNC:903\tGT:DP:AD:GQ:PL:RNC\t0/1:26:15,11:30:30,0,52:.." - ], - [ - "chr16\t520623\tchr16_520623_G_A\tG\tA\t30\t.\tAF=0.5;AQ=30;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000262305|protein_coding||13/13||||||||||1||HGNC|HGNC:17224,A|intron_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000434585|protein_coding||14/14||||||||||1||HGNC|HGNC:17224,A|intron_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000450428|protein_coding||11/11||||||||||1||HGNC|HGNC:17224,A|downstream_gene_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000461009|retained_intron|||||||||||1515|1||HGNC|HGNC:17224,A|downstream_gene_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000464263|retained_intron|||||||||||861|1||HGNC|HGNC:17224,A|downstream_gene_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000487899|retained_intron|||||||||||1605|1||HGNC|HGNC:17224,A|downstream_gene_variant|MODIFIER|LINC00235|ENSG00000277142|Transcript|ENST00000622160|lncRNA|||||||||||4532|-1||HGNC|HGNC:14138\tGT:DP:AD:GQ:PL:RNC\t0/1:18:9,9:30:30,0,51:..", - "chr16\t551632\tchr16_551632_T_C\tT\tC\t57\t.\tAF=1;AQ=57;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|synonymous_variant|LOW|CAPN15|ENSG00000103326|Transcript|ENST00000219611|protein_coding|9/14||||2820|2313|771|G|ggT/ggC|||1||HGNC|HGNC:11182,C|downstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000562370|protein_coding|||||||||||4240|1|cds_end_NF|HGNC|HGNC:11182,C|upstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000565010|retained_intron|||||||||||665|1||HGNC|HGNC:11182,C|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000261691|Transcript|ENST00000565879|lncRNA||1/1||||||||||-1|||,C|upstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000566977|protein_coding|||||||||||1123|1|cds_start_NF|HGNC|HGNC:11182,C|downstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000568988|protein_coding|||||||||||3423|1|cds_end_NF|HGNC|HGNC:11182,C|downstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000637507|protein_coding|||||||||||3601|1|cds_end_NF|HGNC|HGNC:11182\tGT:DP:AD:GQ:PL:RNC\t1/1:13:0,13:39:57,39,0:..", - "chr16\t582180\tchr16_582180_G_C\tG\tC\t40\t.\tAF=1;AQ=40;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000026218|protein_coding||9/9||||||||||1||HGNC|HGNC:14135,C|intron_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000321878|protein_coding||9/10||||||||||1||HGNC|HGNC:14135,C|intron_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000409527|protein_coding||10/11||||||||||1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000420990|nonsense_mediated_decay||6/7||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000422307|protein_coding|||||||||||4946|1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000443147|nonsense_mediated_decay||10/11||||||||||1||HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000470411|protein_coding|||||||||||4963|1||HGNC|HGNC:14135,C|non_coding_transcript_exon_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000476438|retained_intron|1/2||||420|||||||1||HGNC|HGNC:14135,C|intron_variant&non_coding_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000480424|retained_intron||3/4||||||||||1||HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000537901|retained_intron|||||||||||3378|1||HGNC|HGNC:14135,C|intron_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000540241|protein_coding||2/3||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|upstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000540548|protein_coding_CDS_not_defined|||||||||||310|1||HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000544860|protein_coding_CDS_not_defined|||||||||||3337|1||HGNC|HGNC:14135,C|upstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000634341|retained_intron|||||||||||697|1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000635205|nonsense_mediated_decay||3/4||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000635909|nonsense_mediated_decay||8/9||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000635935|protein_coding_CDS_not_defined|||||||||||1403|1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000636005|nonsense_mediated_decay||8/9||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000636657|nonsense_mediated_decay||10/11||||||||||1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000637468|nonsense_mediated_decay||6/7||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000638143|nonsense_mediated_decay|||||||||||1258|1|cds_start_NF|HGNC|HGNC:14135,C|upstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000638152|protein_coding_CDS_not_defined|||||||||||1404|1||HGNC|HGNC:14135\tGT:DP:AD:GQ:PL:RNC\t1/1:6:0,6:16:40,16,0:..", - "chr16\t627629\tchr16_627629_T_C\tT\tC\t57\t.\tAF=1;AQ=57;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|3_prime_UTR_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000248139|protein_coding|6/6||||1079|||||||1||HGNC|HGNC:18285,C|upstream_gene_variant|MODIFIER|WFIKKN1|ENSG00000127578|Transcript|ENST00000319070|protein_coding|||||||||||3356|1||HGNC|HGNC:30912,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000509637|nonsense_mediated_decay|||||||||||1636|1|cds_start_NF|HGNC|HGNC:18285,C|3_prime_UTR_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000535977|protein_coding|7/7||||1075|||||||1||HGNC|HGNC:18285,C|3_prime_UTR_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000538492|protein_coding|7/7||||927|||||||1||HGNC|HGNC:18285,C|3_prime_UTR_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000539661|protein_coding|7/7||||967|||||||1||HGNC|HGNC:18285,C|non_coding_transcript_exon_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000561781|retained_intron|2/2||||796|||||||1||HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000563109|protein_coding|||||||||||46|1|cds_start_NF&cds_end_NF|HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000564703|protein_coding|||||||||||1512|1|cds_end_NF|HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000565511|nonsense_mediated_decay|||||||||||1546|1||HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000566290|protein_coding|||||||||||214|1|cds_end_NF|HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000568586|protein_coding|||||||||||1508|1|cds_end_NF|HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000569575|protein_coding|||||||||||1603|1|cds_end_NF|HGNC|HGNC:18285,C|upstream_gene_variant|MODIFIER|WFIKKN1|ENSG00000127578|Transcript|ENST00000573440|retained_intron|||||||||||1610|1||HGNC|HGNC:30912\tGT:DP:AD:GQ:PL:RNC\t1/1:13:0,13:41:57,41,0:..", - "chr16\t638557\tchr16_638557_A_C\tA\tC\t59\t.\tAF=1;AQ=59;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000301686|protein_coding|||||||||||2252|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000307650|protein_coding|||||||||||3271|1||HGNC|HGNC:14142,C|downstream_gene_variant|MODIFIER|WFIKKN1|ENSG00000127578|Transcript|ENST00000319070|protein_coding|||||||||||4440|1||HGNC|HGNC:30912,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000338401|protein_coding|||||||||||2215|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000397664|protein_coding|||||||||||2206|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000397665|protein_coding|||||||||||2267|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000397666|protein_coding|||||||||||2255|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000448973|retained_intron|||||||||||2247|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000456420|nonsense_mediated_decay|||||||||||2318|-1|cds_start_NF|HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000474840|nonsense_mediated_decay|||||||||||3372|1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000491999|nonsense_mediated_decay|||||||||||3289|1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000564039|nonsense_mediated_decay|||||||||||2279|-1|cds_start_NF|HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000565163|protein_coding|||||||||||2297|-1|cds_start_NF&cds_end_NF|HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000565799|retained_intron|||||||||||2290|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000568077|nonsense_mediated_decay|||||||||||2226|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000568773|protein_coding|||||||||||2322|-1|cds_start_NF|HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000568830|protein_coding|||||||||||2199|-1|cds_end_NF|HGNC|HGNC:14141,C|downstream_gene_variant|MODIFIER|WFIKKN1|ENSG00000127578|Transcript|ENST00000573440|retained_intron|||||||||||4441|1||HGNC|HGNC:30912,C|intron_variant&non_coding_transcript_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000611328|protein_coding_CDS_not_defined||1/3||||||||||1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000614890|protein_coding|||||||||||2191|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000615744|protein_coding_CDS_not_defined|||||||||||3894|1||HGNC|HGNC:14142,C|non_coding_transcript_exon_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000619114|protein_coding_CDS_not_defined|2/2||||576|||||||1||HGNC|HGNC:14142,C|non_coding_transcript_exon_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000619377|protein_coding_CDS_not_defined|2/2||||664|||||||1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000620462|retained_intron|||||||||||3926|1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000629534|protein_coding|||||||||||3292|1||HGNC|HGNC:14142\tGT:DP:AD:GQ:PL:RNC\t1/1:14:0,14:44:59,43,0:..", - "chr16\t655844\tchr16_655844_T_C\tT\tC\t57\t.\tAF=1;AQ=57;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000293879|protein_coding|17/41||||1973|1921|641|L|Ttg/Ctg|||1||HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000420061|retained_intron|17/17||||1985|||||||1||HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000546516|retained_intron|3/20||||614|||||||1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000547407|retained_intron|||||||||||431|1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000548844|protein_coding_CDS_not_defined|||||||||||2716|1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000548859|retained_intron|||||||||||589|1||HGNC|HGNC:26960,C|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000549091|protein_coding|17/41||||2013|1921|641|L|Ttg/Ctg|||1||HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000549648|retained_intron|17/17||||1988|||||||1||HGNC|HGNC:26960,C|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000550593|retained_intron|||||||||||2374|1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000550739|protein_coding|||||||||||3401|1|cds_start_NF&cds_end_NF|HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552648|protein_coding_CDS_not_defined|4/7||||455|||||||1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552683|retained_intron|||||||||||2014|1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552728|nonsense_mediated_decay|||||||||||577|1|cds_start_NF|HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552943|retained_intron|15/26||||3591|||||||1||HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER||ENSG00000262528|Transcript|ENST00000573609|lncRNA|1/2||||351|||||||-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:14:0,14:46:57,46,0:..", - "chr16\t667523\tchr16_667523_G_T\tG\tT\t66\t.\tAF=1;AQ=66;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000293879|protein_coding|41/41||||5233|5181|1727|P|ccG/ccT|||1||HGNC|HGNC:26960,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000315082|protein_coding|||||||||||609|1||HGNC|HGNC:21169,T|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000315764|protein_coding|6/6||||1147|834|278|P|ccG/ccT|||1||HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000546516|retained_intron|||||||||||4090|1||HGNC|HGNC:26960,T|missense_variant|MODERATE|WDR90|ENSG00000161996|Transcript|ENST00000546896|protein_coding|2/2||||89|89|30|R/L|cGt/cTt|||1|cds_start_NF|HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000546923|retained_intron|||||||||||4787|1||HGNC|HGNC:26960,T|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000547407|retained_intron|24/24||||3541|||||||1||HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000547543|protein_coding_CDS_not_defined|||||||||||778|1||HGNC|HGNC:26960,T|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000547944|protein_coding|7/7||||1365|978|326|P|ccG/ccT|||1||HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000548448|retained_intron|||||||||||1162|1||HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000548603|protein_coding_CDS_not_defined|||||||||||4086|1||HGNC|HGNC:26960,T|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000549024|retained_intron|12/12||||1951|||||||1||HGNC|HGNC:26960,T|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000549091|protein_coding|41/41||||5279|5187|1729|P|ccG/ccT|||1||HGNC|HGNC:26960,T|3_prime_UTR_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000551100|protein_coding|3/3||||315|||||||1|cds_start_NF|HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552683|retained_intron|||||||||||4085|1||HGNC|HGNC:26960,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552728|nonsense_mediated_decay|22/22||||2826|||||||1|cds_start_NF|HGNC|HGNC:26960,T|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000553080|retained_intron|6/6||||1635|||||||1||HGNC|HGNC:26960,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000561711|retained_intron|||||||||||4394|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000561929|protein_coding|||||||||||686|1|cds_start_NF&cds_end_NF|HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000561983|nonsense_mediated_decay|||||||||||582|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000562333|nonsense_mediated_decay|||||||||||664|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000562598|retained_intron|||||||||||659|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000562708|retained_intron|||||||||||589|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000563134|protein_coding|||||||||||583|1|cds_end_NF|HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000563637|nonsense_mediated_decay|||||||||||628|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000563776|retained_intron|||||||||||582|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000565004|retained_intron|||||||||||3559|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000566214|nonsense_mediated_decay|||||||||||628|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000566965|retained_intron|||||||||||1037|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000567017|retained_intron|||||||||||639|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000567589|retained_intron|||||||||||3005|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000568636|retained_intron|||||||||||1135|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000568950|retained_intron|||||||||||655|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000569358|retained_intron|||||||||||2932|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000569675|retained_intron|||||||||||612|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000569706|retained_intron|||||||||||609|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000569943|protein_coding_CDS_not_defined|||||||||||830|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000570092|retained_intron|||||||||||601|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000570280|nonsense_mediated_decay|||||||||||630|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000602564|retained_intron|||||||||||657|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000697194|protein_coding|||||||||||577|1||HGNC|HGNC:21169\tGT:DP:AD:GQ:PL:RNC\t1/1:22:0,22:63:66,64,0:..", - "chr16\t690466\tchr16_690466_A_G\tA\tG\t62\t.\tAF=1;AQ=62;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|upstream_gene_variant|MODIFIER|WDR24|ENSG00000127580|Transcript|ENST00000248142|protein_coding|||||||||||22|-1||HGNC|HGNC:20852,G|upstream_gene_variant|MODIFIER|WDR24|ENSG00000127580|Transcript|ENST00000293883|protein_coding|||||||||||68|-1||HGNC|HGNC:20852,G|downstream_gene_variant|MODIFIER|FBXL16|ENSG00000127585|Transcript|ENST00000397621|protein_coding|||||||||||2034|-1||HGNC|HGNC:14150,G|downstream_gene_variant|MODIFIER|FBXL16|ENSG00000127585|Transcript|ENST00000562563|protein_coding|||||||||||2461|-1||HGNC|HGNC:14150,G|downstream_gene_variant|MODIFIER|FBXL16|ENSG00000127585|Transcript|ENST00000562585|protein_coding_CDS_not_defined|||||||||||4192|-1||HGNC|HGNC:14150,G|downstream_gene_variant|MODIFIER|FBXL16|ENSG00000127585|Transcript|ENST00000562648|retained_intron|||||||||||2032|-1||HGNC|HGNC:14150,G|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000261659|Transcript|ENST00000566927|lncRNA||1/1||||||||||1|||,G|upstream_gene_variant|MODIFIER|WDR24|ENSG00000127580|Transcript|ENST00000567014|retained_intron|||||||||||3537|-1||HGNC|HGNC:20852,G|non_coding_transcript_exon_variant|MODIFIER||ENSG00000261659|Transcript|ENST00000575305|retained_intron|1/1||||1466|||||||1|||,G|upstream_gene_variant|MODIFIER|WDR24|ENSG00000127580|Transcript|ENST00000647644|protein_coding|||||||||||219|-1||HGNC|HGNC:20852\tGT:DP:AD:GQ:PL:RNC\t1/1:17:0,17:54:62,54,0:..", - "chr16\t723341\tchr16_723341_G_A\tG\tA\t60\t.\tAF=1;AQ=60;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000219535|protein_coding|||||||||||768|1||HGNC|HGNC:14152,A|intron_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000293889|protein_coding||11/13||||||||||-1||HGNC|HGNC:14153,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000341413|protein_coding|||||||||||3617|1||HGNC|HGNC:14177,A|intron_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000345165|protein_coding||11/13||||||||||-1||HGNC|HGNC:14153,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000389701|retained_intron|||||||||||4064|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000389703|protein_coding|||||||||||3765|1||HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000423653|protein_coding_CDS_not_defined|||||||||||1586|-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000439619|retained_intron|||||||||||1209|-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000460023|retained_intron|||||||||||1566|-1||HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000463539|retained_intron||9/11||||||||||-1||HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000466708|retained_intron||10/12||||||||||-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000471861|retained_intron|||||||||||1660|-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000474647|retained_intron|||||||||||1782|-1||HGNC|HGNC:14153,A|non_coding_transcript_exon_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000478979|retained_intron|4/4||||2296|||||||-1||HGNC|HGNC:14153,A|non_coding_transcript_exon_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000481804|retained_intron|4/5||||2627|||||||-1||HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000482152|retained_intron||3/4||||||||||-1||HGNC|HGNC:14153,A|non_coding_transcript_exon_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000482878|retained_intron|4/4||||2699|||||||-1||HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000485091|retained_intron||10/11||||||||||-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000538176|retained_intron|||||||||||1201|-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000544996|retained_intron|||||||||||1643|-1||HGNC|HGNC:14153,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000549114|protein_coding|||||||||||3595|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000561546|protein_coding|||||||||||3905|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000561750|retained_intron|||||||||||3934|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000562141|protein_coding|||||||||||3778|1|cds_end_NF|HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000562187|protein_coding|||||||||||3765|1|cds_end_NF|HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000563792|protein_coding|||||||||||4398|1|cds_end_NF|HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000564000|protein_coding|||||||||||756|1||HGNC|HGNC:14152,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000564537|protein_coding|||||||||||3765|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000564545|protein_coding|||||||||||3921|1||HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000564640|retained_intron|||||||||||1029|1||HGNC|HGNC:14152,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000566437|retained_intron|||||||||||833|1||HGNC|HGNC:14152,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000566525|retained_intron|||||||||||752|1||HGNC|HGNC:14152,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000567414|protein_coding|||||||||||3952|1|cds_end_NF|HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000567696|retained_intron|||||||||||3977|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000568141|protein_coding|||||||||||4005|1|cds_end_NF|HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|METRN|ENSG00000103260|Transcript|ENST00000568223|protein_coding|||||||||||3686|1||HGNC|HGNC:14151,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000568916|protein_coding|||||||||||751|1|cds_start_NF|HGNC|HGNC:14152,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000569143|retained_intron|||||||||||3977|1||HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000569529|protein_coding|||||||||||751|1||HGNC|HGNC:14152,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000570237|retained_intron|||||||||||751|1||HGNC|HGNC:14152,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000650995|protein_coding|||||||||||2453|-1|cds_end_NF|HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000682391|retained_intron||7/9||||||||||-1||HGNC|HGNC:14153\tGT:DP:AD:GQ:PL:RNC\t1/1:17:0,17:54:60,55,0:..", - "chr16\t739761\tchr16_739761_A_G\tA\tG\t59\t.\tAF=1;AQ=59;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000251588|protein_coding||1/10||||||||||-1||HGNC|HGNC:14179,G|5_prime_UTR_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000540986|protein_coding|1/10||||1174|||||||-1||HGNC|HGNC:14179,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000562421|protein_coding|||||||||||2006|-1|cds_end_NF|HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000562752|retained_intron||1/4||||||||||-1||HGNC|HGNC:14179,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000563534|protein_coding_CDS_not_defined|||||||||||2297|-1||HGNC|HGNC:14179,G|intron_variant&NMD_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000565065|nonsense_mediated_decay||2/5||||||||||-1||HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000565341|retained_intron||1/3||||||||||-1||HGNC|HGNC:14179,G|intron_variant&NMD_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000565425|nonsense_mediated_decay||1/9||||||||||-1||HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000565693|protein_coding_CDS_not_defined||1/2||||||||||-1||HGNC|HGNC:14179,G|intron_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000566614|protein_coding||1/4||||||||||-1|cds_end_NF|HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000567172|protein_coding_CDS_not_defined||1/1||||||||||-1||HGNC|HGNC:14179,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000567403|protein_coding|||||||||||2009|-1|cds_end_NF|HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000567455|protein_coding_CDS_not_defined||1/2||||||||||-1||HGNC|HGNC:14179,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000568545|protein_coding|||||||||||1872|-1||HGNC|HGNC:14179,G|downstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000569604|protein_coding_CDS_not_defined|||||||||||4236|1||HGNC|HGNC:14177,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000569759|protein_coding_CDS_not_defined|||||||||||3391|-1||HGNC|HGNC:14179,G|intron_variant&NMD_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000570066|nonsense_mediated_decay||1/4||||||||||-1||HGNC|HGNC:14179,G|intron_variant&NMD_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000570289|nonsense_mediated_decay||1/3||||||||||-1||HGNC|HGNC:14179,G|downstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000647875|protein_coding_CDS_not_defined|||||||||||4408|1||HGNC|HGNC:14177\tGT:DP:AD:GQ:PL:RNC\t1/1:14:0,14:44:59,43,0:..", - "chr16\t766294\tchr16_766294_T_G\tT\tG\t25\t.\tAF=0.5;AQ=25;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000382862|protein_coding||11/16||||||||||1||HGNC|HGNC:7371,G|upstream_gene_variant|MODIFIER|MIR662|ENSG00000207579|Transcript|ENST00000384847|miRNA|||||||||||3889|1||HGNC|HGNC:32918,G|downstream_gene_variant|MODIFIER|MSLNL|ENSG00000162006|Transcript|ENST00000543963|protein_coding|||||||||||3134|-1|cds_start_NF|HGNC|HGNC:14170,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000545450|protein_coding||12/17||||||||||1||HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000561896|protein_coding||2/6||||||||||1|cds_start_NF&cds_end_NF|HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000563651|protein_coding||10/10||||||||||1|cds_end_NF|HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000563941|protein_coding||12/17||||||||||1||HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000566269|protein_coding||2/7||||||||||1|cds_start_NF|HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000566549|protein_coding||11/16||||||||||1||HGNC|HGNC:7371,G|downstream_gene_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000569566|protein_coding|||||||||||1258|1|cds_end_NF|HGNC|HGNC:7371,G|downstream_gene_variant|MODIFIER||ENSG00000279136|Transcript|ENST00000623562|TEC|||||||||||2825|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:12,7:26:25,0,50:..", - "chr16\t789996\tchr16_789996_T_C\tT\tC\t35\t.\tAF=0.5;AQ=35;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000007264|protein_coding|||||||||||1615|-1||HGNC|HGNC:14173,C|intron_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000262315|protein_coding||4/21||||||||||1||HGNC|HGNC:18435,C|intron_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000317063|protein_coding||4/21||||||||||1||HGNC|HGNC:18435,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|CHTF18|ENSG00000127586|Transcript|ENST00000426047|protein_coding||2/6||||||||||1|cds_start_NF&cds_end_NF|HGNC|HGNC:18435,C|intron_variant&NMD_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000440239|nonsense_mediated_decay||4/13||||||||||1||HGNC|HGNC:18435,C|intron_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000455171|protein_coding||3/20||||||||||1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000461268|protein_coding_CDS_not_defined|||||||||||2528|1||HGNC|HGNC:18435,C|intron_variant&non_coding_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000464728|retained_intron||3/17||||||||||1||HGNC|HGNC:18435,C|splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|CHTF18|ENSG00000127586|Transcript|ENST00000471202|retained_intron||4/18||||||||||1||HGNC|HGNC:18435,C|intron_variant&non_coding_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000479976|retained_intron||4/6||||||||||1||HGNC|HGNC:18435,C|intron_variant&non_coding_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000484349|retained_intron||1/3||||||||||1||HGNC|HGNC:18435,C|intron_variant&non_coding_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000491530|protein_coding_CDS_not_defined||2/5||||||||||1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000493715|protein_coding_CDS_not_defined|||||||||||4706|1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000561734|protein_coding|||||||||||2015|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000562070|protein_coding|||||||||||2527|-1|cds_start_NF|HGNC|HGNC:14173,C|downstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000563545|nonsense_mediated_decay|||||||||||360|1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000563560|protein_coding|||||||||||1667|-1|cds_end_NF|HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000565377|protein_coding|||||||||||1615|-1|cds_end_NF|HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000565503|nonsense_mediated_decay|||||||||||1656|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000565787|retained_intron|||||||||||1141|1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000565809|protein_coding|||||||||||1625|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000567114|protein_coding|||||||||||1599|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000567283|nonsense_mediated_decay|||||||||||1663|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000567620|retained_intron|||||||||||703|1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000569270|nonsense_mediated_decay|||||||||||255|1|cds_start_NF|HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000569601|protein_coding|||||||||||1662|-1|cds_end_NF|HGNC|HGNC:14173,C|downstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000570058|protein_coding_CDS_not_defined|||||||||||656|1||HGNC|HGNC:18435,C|intron_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000631357|protein_coding||5/23||||||||||1||HGNC|HGNC:18435\tGT:DP:AD:GQ:PL:RNC\t0/1:15:7,8:36:35,0,60:..", - "chr16\t813336\tchr16_813336_T_C\tT\tC\t30\t.\tAF=0.5;AQ=30;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER||ENSG00000287855|Transcript|ENST00000655150|lncRNA|||||||||||4153|1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:14:5,9:30:30,0,48:..", - "chr16\t893361\tchr16_893361_T_C\tT\tC\t41\t.\tAF=0.5;AQ=41;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000262301|protein_coding||4/10||||||||||-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000543238|protein_coding||1/7||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||5/11||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562226|nonsense_mediated_decay||6/7||||||||||-1||HGNC|HGNC:14154,C|upstream_gene_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000565198|retained_intron|||||||||||109|-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000566627|protein_coding||3/5||||||||||-1|cds_end_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568897|protein_coding||3/9||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568964|nonsense_mediated_decay||4/5||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||4/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154\tGT:DP:AD:GQ:PL:RNC\t0/1:17:6,11:42:41,0,55:..", - "chr16\t947473\tchr16_947473_T_C\tT\tC\t36\t.\tAF=0.5;AQ=36;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000262301|protein_coding||2/10||||||||||-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000543238|protein_coding||1/7||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||2/11||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562226|nonsense_mediated_decay||2/7||||||||||-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562380|protein_coding||2/3||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|5_prime_UTR_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000566627|protein_coding|1/6||||172|||||||-1|cds_end_NF|HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000567595|nonsense_mediated_decay||2/4||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568897|protein_coding||2/9||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568964|nonsense_mediated_decay||2/5||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||2/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154\tGT:DP:AD:GQ:PL:RNC\t0/1:23:8,15:36:36,0,48:..", - "chr16\t964119\tchr16_964119_A_G\tA\tG\t64\t.\tAF=1;AQ=64;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000262301|protein_coding||1/10||||||||||-1||HGNC|HGNC:14154,G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000543238|protein_coding||1/7||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||1/11||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562226|nonsense_mediated_decay||1/7||||||||||-1||HGNC|HGNC:14154,G|missense_variant|MODERATE|LMF1|ENSG00000103227|Transcript|ENST00000562380|protein_coding|1/4||||4|4|2|Y/H|Tat/Cat|||-1|cds_start_NF|HGNC|HGNC:14154,G|intron_variant&non_coding_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000566609|protein_coding_CDS_not_defined||1/2||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000567595|nonsense_mediated_decay||1/4||||||||||-1|cds_start_NF|HGNC|HGNC:14154,G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568897|protein_coding||1/9||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568964|nonsense_mediated_decay||1/5||||||||||-1|cds_start_NF|HGNC|HGNC:14154,G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||1/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154,G|downstream_gene_variant|MODIFIER||ENSG00000276931|Transcript|ENST00000620075|lncRNA|||||||||||4256|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:29:0,29:61:64,63,0:..", - "chr16\t977069\tchr16_977069_T_C\tT\tC\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|SOX8|ENSG00000005513|Transcript|ENST00000293894|protein_coding|||||||||||4701|1||HGNC|HGNC:11203,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||1/11||||||||||-1||HGNC|HGNC:14154,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000562570|lncRNA|2/2||||1914|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000563837|lncRNA|4/4||||423|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000563863|lncRNA|4/4||||423|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000565069|lncRNA|3/3||||265|||||||-1||HGNC|HGNC:53928,C|upstream_gene_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000565139|lncRNA|||||||||||143|-1||HGNC|HGNC:53928,C|intron_variant&non_coding_transcript_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000565467|lncRNA||1/1||||||||||-1||HGNC|HGNC:53928,C|upstream_gene_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000567961|lncRNA|||||||||||157|-1||HGNC|HGNC:53928,C|intron_variant&non_coding_transcript_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000568394|lncRNA||1/2||||||||||-1||HGNC|HGNC:53928,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||1/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000655952|lncRNA|3/3||||743|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000662104|lncRNA|3/3||||322|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000669274|lncRNA|3/3||||225|||||||-1||HGNC|HGNC:53928\tGT:DP:AD:GQ:PL:RNC\t0/1:17:6,11:35:34,0,58:..", - "chr16\t1065904\tchr16_1065904_G_A\tG\tA\t29\t.\tAF=0.5;AQ=29;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t0/1:15:9,6:29:29,0,48:..", - "chr16\t1221890\tchr16_1221890_G_T\tG\tT\t65\t.\tAF=1;AQ=65;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:18:0,18:54:65,54,0:..", - "chr16\t1261332\tchr16_1261332_A_G\tA\tG\t30\t.\tAF=0.5;AQ=30;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t0/1:16:9,7:30:30,0,47:..", - "chr16\t1324817\tchr16_1324817_A_G\tA\tG\t66\t.\tAF=1;AQ=66;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:24:0,24:62:66,64,0:..", - "chrX\t2917996\tchrX_2917996_G_C\tG\tC\t53\t.\tAF=1;AQ=53;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:10:0,10:30:53,30,0:..", - "chrX\t3024068\tchrX_3024068_T_C\tT\tC\t56\t.\tAF=1;AQ=56;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:13:0,13:39:56,39,0:..", - "chrX\t3084646\tchrX_3084646_A_G\tA\tG\t64\t.\tAF=1;AQ=64;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:16:0,16:54:64,54,0:..", - "chrX\t7057741\tchrX_7057741_C_G\tC\tG\t55\t.\tAF=1;AQ=55;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:11:0,11:34:55,34,0:..", - "chrX\t9946907\tchrX_9946907_G_C\tG\tC\t60\t.\tAF=1;AQ=60;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:15:0,15:49:60,49,0:..", - "chrX\t11139415\tchrX_11139415_G_C\tG\tC\t66\t.\tAF=1;AQ=66;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:20:0,20:59:66,59,0:..", - "chrX\t11182140\tchrX_11182140_G_C\tG\tC\t59\t.\tAF=1;AQ=59;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:14:0,14:46:59,45,0:..", - "chrX\t11760352\tchrX_11760352_G_T\tG\tT\t66\t.\tAF=1;AQ=66;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:21:0,21:61:66,62,0:..", - "chrX\t12609930\tchrX_12609930_T_C\tT\tC\t68\t.\tAF=1;AQ=68;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:22:0,22:65:68,68,0:..", - "chrX\t12791542\tchrX_12791542_G_A\tG\tA\t67\t.\tAF=1;AQ=67;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:20:0,20:58:67,58,0:..", - "chrX\t12820815\tchrX_12820815_A_G\tA\tG\t66\t.\tAF=1;AQ=66;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:18:0,18:58:66,58,0:..", - "chrX\t13785841\tchrX_13785841_C_T\tC\tT\t56\t.\tAF=1;AQ=56;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:14:0,14:43:56,42,0:..", - "chrX\t14581450\tchrX_14581450_A_G\tA\tG\t64\t.\tAF=1;AQ=64;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:16:0,16:56:64,56,0:..", - "chrX\t14609022\tchrX_14609022_T_C\tT\tC\t58\t.\tAF=1;AQ=58;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:14:0,14:41:58,41,0:..", - "chrX\t14850684\tchrX_14850684_A_G\tA\tG\t52\t.\tAF=1;AQ=52;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:16:2,14:26:52,26,0:..", - "chrX\t15397461\tchrX_15397461_C_T\tC\tT\t58\t.\tAF=1;AQ=58;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:12:0,12:38:58,38,0:.." - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-18T11:02:20.581195152" - }, - "bcf, db, vep_cache, '110', -stub": { - "content": [ - [ - "versions.yml:md5,275497de0e23f331b5b5eeb47799c8e9", - "versions.yml:md5,797275193dd19766e99030e63c23bd5f", - "versions.yml:md5,a07924ee4ebc2d4de5bb7ef897ddc30c", - "versions.yml:md5,c0e55e36a31ed71acf25702b7d059533" - ], - [ - [ - { - "id": "multisample" - }, - "multisample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - [ - { - "id": "multisample" - }, - "multisample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-09T10:38:07.171654618" - } -} \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf b/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf index 7bc30f75..93003674 100644 --- a/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf @@ -69,7 +69,7 @@ def workflowDependencies = [ def fileDependencies = [ mapping : ["fasta", "somalier_sites"], assembly : ["fasta", "dipcall_par"], // The assembly workflow should be split into two - assembly and variant calling (requires ref) - snv_annotation : ["snp_db", "vep_cache"], + snv_annotation : ["snp_db", "vep_cache", "reduced_penetrance", "score_config_snv", "variant_consequences_snv"], cnv_calling : ["hificnv_xy", "hificnv_xx", "hificnv_exclude"], repeat_calling : ["trgt_repeats"], repeat_annotation: ["variant_catalog"], @@ -90,16 +90,20 @@ def parameterStatus = [ skip_assembly_wf : params.skip_assembly_wf, ], files: [ - dipcall_par : params.dipcall_par, - snp_db : params.snp_db, - somalier_sites : params.somalier_sites, - vep_cache : params.vep_cache, - hificnv_xy : params.hificnv_xy, - hificnv_xx : params.hificnv_xx, - hificnv_exclude: params.hificnv_exclude, - fasta : params.fasta, - trgt_repeats : params.trgt_repeats, - variant_catalog: params.variant_catalog, + dipcall_par : params.dipcall_par, + snp_db : params.snp_db, + somalier_sites : params.somalier_sites, + vep_cache : params.vep_cache, + hificnv_xy : params.hificnv_xy, + hificnv_xx : params.hificnv_xx, + hificnv_exclude : params.hificnv_exclude, + fasta : params.fasta, + trgt_repeats : params.trgt_repeats, + variant_catalog : params.variant_catalog, + score_config_snv : params.score_config_snv, + reduced_penetrance : params.reduced_penetrance, + score_config_snv : params.score_config_snv, + variant_consequences_snv: params.variant_consequences_snv, ] ] diff --git a/tests/main.nf.test b/tests/main.nf.test index 6023b0a4..14f7020a 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -13,18 +13,22 @@ nextflow_pipeline { // Base directory for genomic-medicine-sweden/nallo test data pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/' // Test files - fasta = params.pipelines_testdata_base_path + 'nallo/reference/hg38.test.fa.gz' - input = params.pipelines_testdata_base_path + 'nallo/testdata/samplesheet.csv' - bed = params.pipelines_testdata_base_path + 'nallo/reference/test_data.bed' - hificnv_xy = params.pipelines_testdata_base_path + 'nallo/reference/expected_cn.hg38.XY.bed' - hificnv_xx = params.pipelines_testdata_base_path + 'nallo/reference/expected_cn.hg38.XX.bed' - hificnv_exclude = params.pipelines_testdata_base_path + 'nallo/reference/empty.bed' - dipcall_par = params.pipelines_testdata_base_path + 'nallo/reference/hs38.PAR.bed' - trgt_repeats = params.pipelines_testdata_base_path + 'nallo/reference/pathogenic_repeats.hg38.bed' - variant_catalog = params.pipelines_testdata_base_path + 'nallo/reference/variant_catalog_grch38.json' - vep_cache = params.pipelines_testdata_base_path + 'nallo/reference/vep_cache_test_data.tar.gz' - snp_db = params.pipelines_testdata_base_path + 'nallo/testdata/snp_dbs.csv' - somalier_sites = params.pipelines_testdata_base_path + 'nallo/reference/somalier_sites.vcf.gz' + fasta = params.pipelines_testdata_base_path + 'nallo/reference/hg38.test.fa.gz' + input = params.pipelines_testdata_base_path + 'nallo/testdata/samplesheet.csv' + bed = params.pipelines_testdata_base_path + 'nallo/reference/test_data.bed' + hificnv_xy = params.pipelines_testdata_base_path + 'nallo/reference/expected_cn.hg38.XY.bed' + hificnv_xx = params.pipelines_testdata_base_path + 'nallo/reference/expected_cn.hg38.XX.bed' + hificnv_exclude = params.pipelines_testdata_base_path + 'nallo/reference/empty.bed' + dipcall_par = params.pipelines_testdata_base_path + 'nallo/reference/hs38.PAR.bed' + trgt_repeats = params.pipelines_testdata_base_path + 'nallo/reference/pathogenic_repeats.hg38.bed' + variant_catalog = params.pipelines_testdata_base_path + 'nallo/reference/variant_catalog_grch38.json' + vep_cache = params.pipelines_testdata_base_path + 'nallo/reference/vep_cache_test_data.tar.gz' + snp_db = params.pipelines_testdata_base_path + 'nallo/testdata/snp_dbs.csv' + somalier_sites = params.pipelines_testdata_base_path + 'nallo/reference/somalier_sites.vcf.gz' + reduced_penetrance = params.pipelines_testdata_base_path + 'nallo/reference/reduced_penetrance.tsv' + score_config_snv = params.pipelines_testdata_base_path + 'nallo/reference/rank_model_snv.ini' + variant_consequences_snv = params.pipelines_testdata_base_path + 'nallo/reference/variant_consequences_v2.txt' + // Parameters parallel_snv = 3 preset = "revio" @@ -89,6 +93,8 @@ nextflow_pipeline { { assert new File("$outputDir/multiqc/multiqc_report.html").exists() }, { assert new File("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists() }, { assert new File("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt").exists() }, + { assert new File("$outputDir/ranked_variants/multisample_snv_ranked.vcf.gz").exists() }, + { assert new File("$outputDir/ranked_variants/multisample_snv_ranked.vcf.gz.tbi").exists() }, { assert new File("$outputDir/repeat_calling/trgt/multi_sample/multisample/multisample.vcf.gz").exists() }, { assert new File("$outputDir/repeat_calling/trgt/multi_sample/multisample/multisample.vcf.gz.tbi").exists() }, { assert new File("$outputDir/snv_annotation/echtvar/encode/multisample/multisample.zip").exists() }, @@ -148,18 +154,22 @@ nextflow_pipeline { // Base directory for genomic-medicine-sweden/nallo test data pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/' // Test files - fasta = params.pipelines_testdata_base_path + 'nallo/reference/hg38.test.fa.gz' - input = params.pipelines_testdata_base_path + 'nallo/testdata/samplesheet_multisample_bam.csv' - bed = params.pipelines_testdata_base_path + 'nallo/reference/test_data.bed' - hificnv_xy = params.pipelines_testdata_base_path + 'nallo/reference/expected_cn.hg38.XY.bed' - hificnv_xx = params.pipelines_testdata_base_path + 'nallo/reference/expected_cn.hg38.XX.bed' - hificnv_exclude = params.pipelines_testdata_base_path + 'nallo/reference/empty.bed' - dipcall_par = params.pipelines_testdata_base_path + 'nallo/reference/hs38.PAR.bed' - trgt_repeats = params.pipelines_testdata_base_path + 'nallo/reference/pathogenic_repeats.hg38.bed' - variant_catalog = params.pipelines_testdata_base_path + 'nallo/reference/variant_catalog_grch38.json' - vep_cache = params.pipelines_testdata_base_path + 'nallo/reference/vep_cache_test_data.tar.gz' - snp_db = params.pipelines_testdata_base_path + 'nallo/testdata/snp_dbs.csv' - somalier_sites = params.pipelines_testdata_base_path + 'nallo/reference/somalier_sites.vcf.gz' + fasta = params.pipelines_testdata_base_path + 'nallo/reference/hg38.test.fa.gz' + input = params.pipelines_testdata_base_path + 'nallo/testdata/samplesheet_multisample_bam.csv' + bed = params.pipelines_testdata_base_path + 'nallo/reference/test_data.bed' + hificnv_xy = params.pipelines_testdata_base_path + 'nallo/reference/expected_cn.hg38.XY.bed' + hificnv_xx = params.pipelines_testdata_base_path + 'nallo/reference/expected_cn.hg38.XX.bed' + hificnv_exclude = params.pipelines_testdata_base_path + 'nallo/reference/empty.bed' + dipcall_par = params.pipelines_testdata_base_path + 'nallo/reference/hs38.PAR.bed' + trgt_repeats = params.pipelines_testdata_base_path + 'nallo/reference/pathogenic_repeats.hg38.bed' + variant_catalog = params.pipelines_testdata_base_path + 'nallo/reference/variant_catalog_grch38.json' + vep_cache = params.pipelines_testdata_base_path + 'nallo/reference/vep_cache_test_data.tar.gz' + snp_db = params.pipelines_testdata_base_path + 'nallo/testdata/snp_dbs.csv' + somalier_sites = params.pipelines_testdata_base_path + 'nallo/reference/somalier_sites.vcf.gz' + reduced_penetrance = params.pipelines_testdata_base_path + 'nallo/reference/reduced_penetrance.tsv' + score_config_snv = params.pipelines_testdata_base_path + 'nallo/reference/rank_model_snv.ini' + variant_consequences_snv = params.pipelines_testdata_base_path + 'nallo/reference/variant_consequences_v2.txt' + // Parameters parallel_snv = 3 preset = "revio" @@ -261,6 +271,8 @@ nextflow_pipeline { { assert new File("$outputDir/multiqc/multiqc_report.html").exists() }, { assert new File("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists() }, { assert new File("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt").exists() }, + { assert new File("$outputDir/ranked_variants/multisample_snv_ranked.vcf.gz").exists() }, + { assert new File("$outputDir/ranked_variants/multisample_snv_ranked.vcf.gz.tbi").exists() }, { assert new File("$outputDir/snv_annotation/echtvar/encode/multisample/multisample.zip").exists() }, { assert new File("$outputDir/snv_annotation/vep/multi_sample/multisample/multisample_vep.vcf.gz").exists() }, { assert new File("$outputDir/snv_annotation/vep/multi_sample/multisample/multisample_vep.vcf.gz.tbi").exists() }, diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap index 698c6b44..ea6b5c55 100644 --- a/tests/main.nf.test.snap +++ b/tests/main.nf.test.snap @@ -50,7 +50,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-17T19:59:10.02085362" + "timestamp": "2024-07-18T11:31:11.633360548" }, "test profile - multisample": { "content": [ @@ -135,6 +135,6 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-17T20:03:09.938862526" + "timestamp": "2024-07-18T11:35:11.131546288" } } \ No newline at end of file diff --git a/workflows/nallo.nf b/workflows/nallo.nf index 467bebb2..c44d7eb4 100644 --- a/workflows/nallo.nf +++ b/workflows/nallo.nf @@ -6,22 +6,24 @@ include { fromSamplesheet } from 'plugin/nf-validation' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { ANNOTATE_REPEAT_EXPANSIONS } from '../subworkflows/local/annotate_repeat_expansions' -include { ASSEMBLY } from '../subworkflows/local/genome_assembly' -include { ASSEMBLY_VARIANT_CALLING } from '../subworkflows/local/assembly_variant_calling' -include { BAM_TO_FASTQ } from '../subworkflows/local/bam_to_fastq' -include { BAM_INFER_SEX } from '../subworkflows/local/bam_infer_sex' -include { CALL_PARALOGS } from '../subworkflows/local/call_paralogs' -include { CALL_REPEAT_EXPANSIONS } from '../subworkflows/local/call_repeat_expansions' -include { CNV } from '../subworkflows/local/cnv' -include { METHYLATION } from '../subworkflows/local/methylation' -include { PHASING } from '../subworkflows/local/phasing' -include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome' -include { QC_ALIGNED_READS } from '../subworkflows/local/qc_aligned_reads' -include { SCATTER_GENOME } from '../subworkflows/local/scatter_genome' -include { SHORT_VARIANT_CALLING } from '../subworkflows/local/short_variant_calling' -include { SNV_ANNOTATION } from '../subworkflows/local/snv_annotation' -include { STRUCTURAL_VARIANT_CALLING } from '../subworkflows/local/structural_variant_calling' +include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_SNV } from '../subworkflows/local/annotate_consequence_pli' +include { ANNOTATE_REPEAT_EXPANSIONS } from '../subworkflows/local/annotate_repeat_expansions' +include { ASSEMBLY } from '../subworkflows/local/genome_assembly' +include { ASSEMBLY_VARIANT_CALLING } from '../subworkflows/local/assembly_variant_calling' +include { BAM_TO_FASTQ } from '../subworkflows/local/bam_to_fastq' +include { BAM_INFER_SEX } from '../subworkflows/local/bam_infer_sex' +include { CALL_PARALOGS } from '../subworkflows/local/call_paralogs' +include { CALL_REPEAT_EXPANSIONS } from '../subworkflows/local/call_repeat_expansions' +include { CNV } from '../subworkflows/local/cnv' +include { METHYLATION } from '../subworkflows/local/methylation' +include { PHASING } from '../subworkflows/local/phasing' +include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome' +include { QC_ALIGNED_READS } from '../subworkflows/local/qc_aligned_reads' +include { RANK_VARIANTS as RANK_VARIANTS_SNV } from '../subworkflows/local/rank_variants' +include { SCATTER_GENOME } from '../subworkflows/local/scatter_genome' +include { SHORT_VARIANT_CALLING } from '../subworkflows/local/short_variant_calling' +include { SNV_ANNOTATION } from '../subworkflows/local/snv_annotation' +include { STRUCTURAL_VARIANT_CALLING } from '../subworkflows/local/structural_variant_calling' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -72,29 +74,36 @@ workflow NALLO { : Channel.value([[],[]]) // Conditional input files that has to be set depending on which workflow is run - ch_par = params.dipcall_par ? Channel.fromPath(params.dipcall_par).collect() - : '' - ch_trgt_bed = params.trgt_repeats ? Channel.fromPath(params.trgt_repeats).map { it -> [ it.simpleName, it ] }.collect() - : '' - ch_variant_catalog = params.variant_catalog ? Channel.fromPath(params.variant_catalog).map { it -> [ it.simpleName, it ] }.collect() - : '' - ch_databases = params.snp_db ? Channel.fromSamplesheet('snp_db', immutable_meta: false).map{ it[1] }.collect() - : '' - ch_vep_cache_unprocessed = params.vep_cache ? Channel.fromPath(params.vep_cache).map { it -> [ [id:'vep_cache'], it ] }.collect() - : Channel.value([[],[]]) - ch_expected_xy_bed = params.hificnv_xy ? Channel.fromPath(params.hificnv_xy).collect() - : '' - ch_expected_xx_bed = params.hificnv_xx ? Channel.fromPath(params.hificnv_xx).collect() - : '' - ch_exclude_bed = params.hificnv_exclude ? Channel.fromPath(params.hificnv_exclude).collect() - : '' - ch_somalier_sites = params.somalier_sites ? Channel.fromPath(params.somalier_sites).map { [it.simpleName, it ] }.collect() - : '' + ch_par = params.dipcall_par ? Channel.fromPath(params.dipcall_par).collect() + : '' + ch_trgt_bed = params.trgt_repeats ? Channel.fromPath(params.trgt_repeats).map { it -> [ it.simpleName, it ] }.collect() + : '' + ch_variant_catalog = params.variant_catalog ? Channel.fromPath(params.variant_catalog).map { it -> [ it.simpleName, it ] }.collect() + : '' + // TODO: Add all missing parameters to schema + ch_databases = params.snp_db ? Channel.fromSamplesheet('snp_db', immutable_meta: false).map{ it[1] }.collect() + : '' + ch_variant_consequences_snv = params.variant_consequences_snv ? Channel.fromPath(params.variant_consequences_snv).collect() + : Channel.value([]) + ch_vep_cache_unprocessed = params.vep_cache ? Channel.fromPath(params.vep_cache).map { it -> [ [id:'vep_cache'], it ] }.collect() + : Channel.value([[],[]]) + ch_expected_xy_bed = params.hificnv_xy ? Channel.fromPath(params.hificnv_xy).collect() + : '' + ch_expected_xx_bed = params.hificnv_xx ? Channel.fromPath(params.hificnv_xx).collect() + : '' + ch_exclude_bed = params.hificnv_exclude ? Channel.fromPath(params.hificnv_exclude).collect() + : '' + ch_reduced_penetrance = params.reduced_penetrance ? Channel.fromPath(params.reduced_penetrance).collect() + : Channel.value([]) + ch_score_config_snv = params.score_config_snv ? Channel.fromPath(params.score_config_snv).collect() + : Channel.value([]) + ch_somalier_sites = params.somalier_sites ? Channel.fromPath(params.somalier_sites).map { [it.simpleName, it ] }.collect() + : '' // Check parameter that doesn't conform to schema validation here - if (params.split_fastq != 0 && (params.split_fastq < 2 || params.split_fastq > 999 )) { exit 1, '--split_fastq must be 0, or between 2 and 999'} - if (params.parallel_snv == 0 ) { exit 1, '--parallel_snv must be > 0'} - if (params.phaser.matches('hiphase_sv|hiphase_snv') && params.preset == 'ONT_R10') { exit 1, 'The HiPhase license only permits analysis of data from PacBio. For details see: https://github.com/PacificBiosciences/HiPhase/blob/main/LICENSE.md' } + if (params.split_fastq != 0 && (params.split_fastq < 2 || params.split_fastq > 999 )) { error "--split_fastq must be 0, or between 2 and 999."} + if (params.parallel_snv == 0 ) { error "--parallel_snv must be > 0." } + if (params.phaser.matches('hiphase_sv|hiphase_snv') && params.preset == 'ONT_R10') { error "The HiPhase license only permits analysis of data from PacBio. For details see: https://github.com/PacificBiosciences/HiPhase/blob/main/LICENSE.md" } // Create PED from samplesheet ch_pedfile = ch_input.toList().map { file(CustomFunctions.makePed(it, params.outdir)) } @@ -310,6 +319,25 @@ workflow NALLO { [], [] ) + + ANN_CSQ_PLI_SNV ( + SNV_ANNOTATION.out.vcf, + ch_variant_consequences_snv + ) + ch_versions = ch_versions.mix(ANN_CSQ_PLI_SNV.out.versions) + + ANN_CSQ_PLI_SNV.out.vcf_ann + .filter { meta, vcf -> meta.contains_affected } + .set { ch_rank_variants_in } + + // Only run on if we have affected individuals + RANK_VARIANTS_SNV ( + ch_rank_variants_in, + ch_pedfile, + ch_reduced_penetrance, + ch_score_config_snv + ) + ch_versions = ch_versions.mix(RANK_VARIANTS_SNV.out.versions) } if(!params.skip_cnv_calling) {