From 6f41281d17560f251d17b6935e43ca065b4dd771 Mon Sep 17 00:00:00 2001 From: Patrik Smeds Date: Fri, 9 Feb 2024 13:31:02 +0100 Subject: [PATCH 01/40] feat: hg38 config and reference file setup --- config/config.data.hg38.yaml | 20 +- config/references/design_files.hg38.yaml | 193 + config/references/nextseq.hg38.pon.yaml | 63 + config/references/novaseq.hg38.pon.yaml | 65 + config/references/references.hg19.yaml | 19 +- config/references/references.hg38.yaml | 12907 +++++++++++++++++++++ 6 files changed, 13244 insertions(+), 23 deletions(-) create mode 100644 config/references/design_files.hg38.yaml create mode 100644 config/references/nextseq.hg38.pon.yaml create mode 100644 config/references/novaseq.hg38.pon.yaml create mode 100644 config/references/references.hg38.yaml diff --git a/config/config.data.hg38.yaml b/config/config.data.hg38.yaml index d4866b2f..e7ed2052 100644 --- a/config/config.data.hg38.yaml +++ b/config/config.data.hg38.yaml @@ -7,27 +7,27 @@ reference: background: "{{PROJECT_PON_DATA}}/GMS560/Background/background_panel_nextseq_noUmea_27_dp500_af015_hg38.tsv" artifacts: "{{PROJECT_PON_DATA}}/GMS560/Artifact/artifact_panel_nextseq_noUmea_27_hg38.tsv" fasta: "{{PROJECT_REF_DATA}}/ref_data/GRCh38_p14/homo_sapiens.fasta" - fasta_rna: "{{PROJECT_REF_DATA}}/ref_data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa" + fasta_rna: "{{PROJECT_REF_DATA}}/ref_data/star-fusion/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa" dict: "{{PROJECT_REF_DATA}}/ref_data/GRCh38_p14/homo_sapiens.fasta.dict" fai: "{{PROJECT_REF_DATA}}/ref_data/GRCh38_p14/homo_sapiens.fasta.fai" design_bed: "{{PROJECT_DESIGN_DATA}}/GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed" design_intervals: "{{PROJECT_DESIGN_DATA}}/GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.interval_list" design_intervals_gatk_cnv: "{{PROJECT_DESIGN_DATA}}/GMS560/design/gatk.design.hg38.preprocessed.interval_list" - design_bed_rna: "{{PROJECT_DESIGN_DATA}}/GMS560/design/Twist_RNA_Design5.annotated_hg38.bed" + design_bed_rna: "{{PROJECT_DESIGN_DATA}}/GMS560/design/Twist_RNA_Design5.annotated.hg38.bed" design_intervals_rna: "{{PROJECT_DESIGN_DATA}}/GMS560/design/Twist_RNA_Design5.annotated.hg38.interval_list" skip_chrs: - "chrM" arriba: assembly: "{{PROJECT_REF_DATA}}/ref_data/GRCh38_p14/homo_sapiens.fasta" - blacklist: "{{PROJECT_REF_DATA}}/ref_data/arriba_v2.3.0_hg38/blacklist_hg38_GRCh38_v2.3.0.tsv.gz" + blacklist: "{{PROJECT_REF_DATA}}/ref_data/arriba_v2.3.0/blacklist_hg38_GRCh38_v2.3.0.tsv.gz" gtf: "{{PROJECT_REF_DATA}}/ref_data/refGene/hg38.refGene.gtf" - extra: "-p {{PROJECT_REF_DATA}}/ref_data/arriba_v2.3.0_hg38/protein_domains_hg38_GRCh38_v2.3.0.gff3 -k {{PROJECT_REF_DATA}}/ref_data/arriba_v2.3.0_hg38/known_fusions_hg38_GRCh38_v2.3.0.tsv.gz" + extra: "-p {{PROJECT_REF_DATA}}/ref_data/arriba_v2.3.0/protein_domains_hg38_GRCh38_v2.3.0.gff3 -k {{PROJECT_REF_DATA}}/ref_data/arriba_v2.3.0/known_fusions_hg38_GRCh38_v2.3.0.tsv.gz" arriba_draw_fusion: - cytobands: "{{PROJECT_REF_DATA}}/ref_data/arriba_v2.3.0_hg38/cytobands_hg38_GRCh38_v2.3.0.tsv" + cytobands: "{{PROJECT_REF_DATA}}/ref_data/arriba_v2.3.0/cytobands_hg38_GRCh38_v2.3.0.tsv" gtf: "{{PROJECT_REF_DATA}}/ref_data/refGene/hg38.refGene.gtf" - protein_domains: "{{PROJECT_REF_DATA}}/ref_data/arriba_v2.3.0_hg38/protein_domains_hg38_GRCh38_v2.3.0.gff3" + protein_domains: "{{PROJECT_REF_DATA}}/ref_data/arriba_v2.3.0/protein_domains_hg38_GRCh38_v2.3.0.gff3" annotate_cnv: cnv_amp_genes: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes_hg38.bed" @@ -66,7 +66,7 @@ cnvkit_batch_hrd: normal_reference_hrd: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_nextseq_noUmea_27_hg38.cnn" exon_skipping: - design_bed: "{{PROJECT_DESIGN_DATA}}/GMS560/design/Twist_RNA_Design5.annotated_hg38.bed" + design_bed: "{{PROJECT_DESIGN_DATA}}/GMS560/design/Twist_RNA_Design5.annotated.hg38.bed" filter_fuseq_wes: gene_fusion_black_list: "{{PROJECT_DESIGN_DATA}}/GMS560/fuseq_wes/false_positive_fusion_pairs.txt" @@ -120,8 +120,8 @@ msisensor_pro: PoN: "{{PROJECT_PON_DATA}}/GMS560/PoN/Msisensor_pro_reference_nextseq_noUmea_27_hg38.list_baseline" purecn: - extra: "--model betabin --mapping-bias-file {{PROJECT_PON_DATA}}/GMS560/PoN/purecn/mapping_bias_hg38.rds" - normaldb: "{{PROJECT_PON_DATA}}/GMS560/PoN/purecn/normalDB_hg38.rds" + extra: "--model betabin --mapping-bias-file {{PROJECT_PON_DATA}}/GMS560/PoN/purecn/mapping_bias_nextseq_hg38.rds" + normaldb: "{{PROJECT_PON_DATA}}/GMS560/PoN/purecn/normalDB_nextseq_hg38.rds" intervals: "{{PROJECT_DESIGN_DATA}}/GMS560/purecn/targets_twist-gms-st_hg38_25000_intervals.txt" purecn_coverage: @@ -135,7 +135,7 @@ scarhrd: reference_name: "grch38" star: - genome_index: "{{PROJECT_REF_DATA}}/ref_data/star/v2.7.10a_hg38/" + genome_index: "{{PROJECT_REF_DATA}}/ref_data/star/STAR_v2.7.10a_hg38/" extra: "--quantMode GeneCounts --sjdbGTFfile {{PROJECT_REF_DATA}}/ref_data/refGene/hg38.refGene.gtf --outSAMtype BAM SortedByCoordinate --chimSegmentMin 10 --chimOutType WithinBAM SoftClip --chimJunctionOverhangMin 10 --chimScoreMin 1 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentReadGapMax 3" star_fusion: diff --git a/config/references/design_files.hg38.yaml b/config/references/design_files.hg38.yaml new file mode 100644 index 00000000..4e44c944 --- /dev/null +++ b/config/references/design_files.hg38.yaml @@ -0,0 +1,193 @@ +--- + + annotate_cnv: + cnv_amp_genes: + path: GMS560/cnv/cnv_amp_genes_hg38.bed + checksum: 51ca611484f5b406edfe79f06e8879ef + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/cnv_amp_genes_hg38.bed + + cnv_loh_genes_all: + path: GMS560/cnv/cnv_loh_genes_hg38.bed + checksum: 219ec534eb7bf5e617a8d4d11a18ca24 + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/cnv_loh_genes_hg38.bed + + cnv_loh_genes_validated: + path: GMS560/cnv/cnv_loh_uppsala_genes_hg38.bed + checksum: 88026108ccf28766e12385a356fffd21 + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/cnv_loh_uppsala_genes_hg38.bed + + bcftools_filter_include_region: + exon: + path: GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.bed + checksum: 720e34fbe7d559980a283cc2839c559a + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.bed + + bcftools_filter_exclude_region: + blacklist: + checksum: 3911faef7fd360a7960841d2ba4b6054 + path: GMS560/cnv/cnvkit_germline_blacklist_20221221_hg38.bed + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/cnvkit_germline_blacklist_20221221_hg38.bed + + bcftools_id_snps: + snps_bed: + checksum: 907d2ba6fcac9b33b5a4fcdef0eedb66 + path: GMS560/design/ID_SNPs_hg38.bed + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/ID_SNPs_hg38.bed + + call_small_cnv_amplifications: + regions_file: + checksum: 4f7b0d50c0acc18201512e59322c144c + path: GMS560/cnv/cnv_amplification_genes_hg38.tsv + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/cnv_amplification_genes_hg38.tsv + + call_small_cnv_deletions: + regions_file: + checksum: 92510485ce32e9ef64697121aae4122c + path: GMS560/cnv/cnv_deletion_genes_hg38.tsv + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/cnv_deletion_genes_hg38.tsv + + exon_skipping: + design_bed: + checksum: 75299f3690fd91d8e42e7db3743896b2 + path: GMS560/design/Twist_RNA_Design5.annotated.hg38.bed + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/Twist_RNA_Design5.annotated.hg38.bed + + filter_fuseq_wes: + gene_white_list: + checksum: d762e65cc9d9d01d022db7de7c31cc68 + path: GMS560/fuseq_wes/fuseq_wes_gene_white_list.txt + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.1/fuseq_wes/fuseq_wes_gene_white_list.txt + + transcript_black_list: + checksum: 586ad13ce609fdf5390d299cbbaae183 + path: GMS560/fuseq_wes/fuseq_wes_transcript_black_list.txt + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.1/fuseq_wes/fuseq_wes_transcript_black_list.txt + + gene_fusion_black_list: + checksum: 21f8b965c1404f6ec4088d3816421809 + path: GMS560/fuseq_wes/false_positive_fusion_pairs.txt + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.4.0/fuseq_wes/false_positive_fusion_pairs.txt + + fuseq_wes: + params: + checksum: d2e6d449027c49e24f026261082fa5bb + path: GMS560/fuseq_wes/fuseq_params.txt + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.1/fuseq_wes/fuseq_params.txt + + gatk_collect_allelic_counts: + SNP_interval: + checksum: 32f3be3365e485092c33e9f0997968c1 + path: GMS560/cnv/gnomad_SNP_0.001_target.annotated.hg38.interval_list + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/gnomad_SNP_0.001_target.annotated.hg38.interval_list + + hotspot_annotation: + hotspots: + checksum: 08c574ec13984188c8e4d2c80c14d2e3 + path: GMS560/reports/Hotspots_combined_regions_nodups.231011_hg38.csv + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/Hotspots_combined_regions_nodups.231011_hg38.csv + + hotspot_info: + hotspot_mutations: + checksum: 08c574ec13984188c8e4d2c80c14d2e3 + path: GMS560/reports/Hotspots_combined_regions_nodups.231011_hg38.csv + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/Hotspots_combined_regions_nodups.231011_hg38.csv + + hotspot_report: + hotspot_mutations: + checksum: 08c574ec13984188c8e4d2c80c14d2e3 + path: GMS560/reports/Hotspots_combined_regions_nodups.231011_hg38.csv + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/Hotspots_combined_regions_nodups.231011_hg38.csv + + manta_config_t: + extra: + checksum: 15dc3d83cba8ffbb8e5226ae38b26da8 + path: GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed.gz + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed.gz + extra_tbi: + checksum: 2c76712f672c4bf7f05eba12314ff61d + path: GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed.gz.tbi + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed.gz.tbi + + purecn: + intervals: + checksum: af529c0ece5fe201de4d507000564ff7 + path: GMS560/purecn/targets_twist-gms-st_hg38_25000_intervals.txt + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/targets_twist-gms-st_hg38_25000_intervals.txt + + purecn_coverage: + intervals: + checksum: af529c0ece5fe201de4d507000564ff7 + path: GMS560/purecn/targets_twist-gms-st_hg38_25000_intervals.txt + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/targets_twist-gms-st_hg38_25000_intervals.txt + + report_fusions: + annotation_bed: + checksum: af529c0ece5fe201de4d507000564ff7 + path: GMS560/design/Twist_RNA_fusionpartners_hg38.bed + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/rna_fusion/Twist_RNA_fusionpartners.bed + + fp_fusions: + checksum: eca1c1cf1f1e068cbdada20bdb75c392 + path: GMS560/rna_fusion/filter_rna_fusions_20231024.txt + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/rna_fusion/filter_rna_fusions_20231024.txt + + references: + design_bed: + checksum: ad95a96bfb3416ce6d2aadf6e3df207c + path: GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed + + design_intervals: + checksum: 509c6f79e136b8c3de8dbe5b63c29fb0 + path: GMS560/design//pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.interval_list + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design//pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.interval_list + + design_intervals_gatk_cnv: + checksum: 58088e1c88e02f7b0cfd5211eabc01cd + path: GMS560/design/gatk.design.hg38.preprocessed.interval_list + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/gatk.design.hg38.preprocessed.interval_list + + design_bed_rna: + checksum: ad95a96bfb3416ce6d2aadf6e3df207c + path: GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed + + design_intervals_rna: + checksum: 2d05715acc2a54f11e8c2ead3126d76e + path: GMS560/design/Twist_RNA_Design5.annotated.hg38.interval_list + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/Twist_RNA_Design5.annotated.hg38.interval_list + + tmb: + filter_genes: + checksum: c1a958320451fab1200ab769d963d4c6 + path: GMS560/tmb/tmb_filter_genes.txt + type: file + url: https://raw.githubusercontent.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/v0.2.1/tmb/tmb_filter_genes.txt diff --git a/config/references/nextseq.hg38.pon.yaml b/config/references/nextseq.hg38.pon.yaml new file mode 100644 index 00000000..7dbad80a --- /dev/null +++ b/config/references/nextseq.hg38.pon.yaml @@ -0,0 +1,63 @@ +--- + + svdb_query: + db_string: + checksum: 0d7a6e99022ef92f54b90de79560577c + path: GMS560/PoN/SVDB/all_T_185_svdb_0.8_hg38_20240214.vcf + type: file + url: https://figshare.com/ndownloader/files/44544002?private_link=53f1597211477d840a29 + + purecn: + extra: + checksum: 71da81a7c80a06a7ec455271d9a21884 + path: GMS560/PoN/purecn/mapping_bias_nextseq_hg38.rds + type: file + url: https://figshare.com/ndownloader/files/44486711?private_link=53f1597211477d840a29 + + normaldb: + checksum: 542e377a41834e9123b88800cfbd381c + path: GMS560/PoN/purecn/normalDB_nextseq_hg38.rds + type: file + url: https://figshare.com/ndownloader/files/44486714?private_link=53f1597211477d840a29 + + + gatk_denoise_read_counts: + normal_reference: + checksum: 8a06c6f84bb01e4feadb92c35c556a62 + path: GMS560/PoN/gatk_cnv_nextseq_27_hg38.hdf5 + type: file + url: https://figshare.com/ndownloader/files/44525696?private_link=53f1597211477d840a29 + + cnvkit_batch: + normal_reference: + checksum: b9995ea0cfa1c259fe7229aee1fd2646 + path: GMS560/PoN/cnvkit_nextseq_noUmea_27_hg38.cnn + type: file + url: https://figshare.com/ndownloader/files/44328734?private_link=53f1597211477d840a29 + + #cnvkit_batch_hrd: + # normal_reference_hrd: + # checksum: + # path: GMS560/PoN/XXXX_hg38.cnn + # type: file + # url: + + msisensor_pro: + PoN: + checksum: 62f5e1ce5c242013af8398ba427314d7 + path: GMS560/PoN/Msisensor_pro_reference_nextseq_noUmea_27_hg38.list_baseline + type: file + url: https://figshare.com/ndownloader/files/44328716?private_link=53f1597211477d840a29 + + reference: + background: + checksum: 1180c940991a8cf9a232b364ca6934a8 + path: GMS560/Background/background_panel_nextseq_noUmea_27_dp500_af015_hg38.tsv + type: file + url: https://figshare.com/ndownloader/files/44328743?private_link=53f1597211477d840a29 + + artifacts: + checksum: b4ca00ae1046cb13c2cd4ec38b4b7308 + path: GMS560/Artifact/artifact_panel_nextseq_noUmea_27_hg38.tsv + type: file + url: https://figshare.com/ndownloader/files/44328728?private_link=53f1597211477d840a29 diff --git a/config/references/novaseq.hg38.pon.yaml b/config/references/novaseq.hg38.pon.yaml new file mode 100644 index 00000000..edcd8ce9 --- /dev/null +++ b/config/references/novaseq.hg38.pon.yaml @@ -0,0 +1,65 @@ +--- + +## We need to create files for NovaSeq +# svdb_query: +# db_string: +# checksum: +# path: GMS560/PoN/SVDB/all_TN_292_svdb_0.8_20220505.vcf +# type: file +# url: + +# purecn: +# extra: +# checksum: 4050b046b37d2c8ae600f3fe8c49922f +# path: GMS560/PoN/purecn/purecn_mapping_bias_Lund_8HRD_samples.rds +# type: file +# url: https://figshare.com/ndownloader/files/44328710?private_link=53f1597211477d840a29 + +# normaldb: +# checksum: 1970ef0831cab6328df954b9e9482b54 +# path: GMS560/PoN/purecn/purecn_normal_db_Lund_8HRD_samples.rds +# type: file +# url: https://figshare.com/ndownloader/files/44328722?private_link=53f1597211477d840a29 + + +# gatk_denoise_read_counts: +# normal_reference: +# checksum: e353bb1a647a0240fbd0107ce5b01e6d +# path: GMS560/PoN/gatk_cnv_novaseq_13_hg38.hdf5 +# type: file +# url: https://figshare.com/ndownloader/files/44328719?private_link=53f1597211477d840a29 + +# cnvkit_batch: +# normal_reference: +# checksum: 8aac23e2ed093ef6bb8a94c5d181a595 +# path: GMS560/PoN/cnvkit_novaseq_13_hg38.cnn +# type: file +# url: https://figshare.com/ndownloader/files/44328731?private_link=53f1597211477d840a29 + +# cnvkit_batch_hrd: +# normal_reference_hrd: +# checksum: +# path: GMS560/PoN/cnvkit_novaseq_13_HRD.cnn +# type: file +# url: https://figshare.com/ndownloader/files/44328713?private_link=53f1597211477d840a29 + +# msisensor_pro: +# PoN: +# checksum: 8b5ea989a5c617aaa1ab1f81ec525e8b +# path: GMS560/PoN/Msisensor_pro_reference_novaseq_13_hg38.list_baseline +# type: file +# url: https://figshare.com/ndownloader/files/44328713?private_link=53f1597211477d840a29 + +# reference: +# background: +# checksum: 1180c940991a8cf9a232b364ca6934a8 +# path: GMS560/Background/background_panel_novaseq_13_dp500_af015_hg38.tsv +# type: file +# url: https://figshare.com/ndownloader/files/44328740?private_link=53f1597211477d840a29 + +# artifacts: +# checksum: b4ca00ae1046cb13c2cd4ec38b4b7308 +# path: GMS560/Artifact/artifact_panel_novaseq_13_hg38.tsv +# type: file +# url: https://figshare.com/ndownloader/files/44328725?private_link=53f1597211477d840a29 + diff --git a/config/references/references.hg19.yaml b/config/references/references.hg19.yaml index 58a85aaa..07a07e2d 100644 --- a/config/references/references.hg19.yaml +++ b/config/references/references.hg19.yaml @@ -6,7 +6,7 @@ path: ref_data/arriba_v2.3.0 type: folder content_checksum: - blacklist_hg19_hs37d5_GRCh37_v2.3.0.tsv.gz: ca7b0b42ec2498814a5c408a5477e052 + : ca7b0b42ec2498814a5c408a5477e052 cytobands_hg19_hs37d5_GRCh37_v2.3.0.tsv: 9333eaa96c56fa22624ab432b8391b2b known_fusions_hg19_hs37d5_GRCh37_v2.3.0.tsv.gz: 2f063a0065c1c88d86c859b924d8d590 protein_domains_hg19_hs37d5_GRCh37_v2.3.0.gff3: b5bc63c70c9eb08c71528ee8b0186901 @@ -101,14 +101,7 @@ path: ref_data/GNOMAD/small_exac_common_3.hg19.vcf.gz.tbi type: file url: https://figshare.scilifelab.se/ndownloader/files/42061254 - - gene_fuse: - fasta: - checksum: 7c1739fd43764bd5e3b9b76ce8635bf0 - path: ref_data/hg19/hg19.with.mt.fasta - type: file - url: https://figshare.scilifelab.se/ndownloader/files/42060171 - + references: fasta: checksum: 7c1739fd43764bd5e3b9b76ce8635bf0 @@ -318,7 +311,7 @@ compressed_checksum: 96954f4f0fdf3c89fed6d8143aef3412 path: ref_data/star type: folder - checksum_content: + content_checksum: v2.7.10a_hg19/exonInfo.tab: 1765bb10b661ae85f2187f10f0013c6a v2.7.10a_hg19/SA: 90569083f6334b60f98990b345ef30d5 v2.7.10a_hg19/exonGeTrInfo.tab: e361a44a5fb8cde31953c10de9bc0fc7 @@ -393,12 +386,12 @@ vep: vep_cache: compressed_checksum: 6eb952ad8c1003b7e1a9b011771fae9e - path: ref_data/vep/105 + path: ref_data/vep/105/homo_sapiens_refseq type: folder content_checksum: - homo_sapiens_refseq/105_GRCh37/HG1463_PATCH/114000001-115000000_reg.gz: c01d9c84f552841842da29450cbe3e9f + 105_GRCh37/HG1463_PATCH/114000001-115000000_reg.gz: c01d9c84f552841842da29450cbe3e9f homo_sapiens_refseq/105_GRCh37/HG1463_PATCH/all_vars.gz: 7a6c597ec65c982c80fe0ab89a071d59 - homo_sapiens_refseq/105_GRCh37/HG1463_PATCH/114000001-115000000.gz: 876549f369d9c55811216e29f7d0cd19 + /105_GRCh37/HG1463_PATCH/114000001-115000000.gz: 876549f369d9c55811216e29f7d0cd19 homo_sapiens_refseq/105_GRCh37/HG1463_PATCH/115000001-116000000_reg.gz: 49865f8fa24479ca5342ce7df5b082d0 homo_sapiens_refseq/105_GRCh37/HG1463_PATCH/all_vars.gz.csi: 66f720e01f5b9f4fefd97225e590aa7c homo_sapiens_refseq/105_GRCh37/HG1463_PATCH/115000001-116000000.gz: bf658fd769d3abd02c07be1538505e36 diff --git a/config/references/references.hg38.yaml b/config/references/references.hg38.yaml new file mode 100644 index 00000000..d23fce29 --- /dev/null +++ b/config/references/references.hg38.yaml @@ -0,0 +1,12907 @@ +--- + + arriba: + data_folder: + compressed_checksum: 1e75410b8c3613180fba7076f7cdf520 + path: ref_data/arriba_v2.3.0 + type: folder + content_checksum: + blacklist_hg38_GRCh38_v2.3.0.tsv.gz: 8c6899e83e7509ed6b745f17667bd93a + cytobands_hg38_GRCh38_v2.3.0.tsv: 7bd504feefb33fcfc9be0517439a423c + known_fusions_hg38_GRCh38_v2.3.0.tsv.gz: 2d6975f9c9379085d67f44cf45eac15f + protein_domains_hg38_GRCh38_v2.3.0.gff3: 43c387a784ebeed71b4147076cebf978 + url: https://figshare.com/ndownloader/files/44328410?private_link=7084cf61820c148a23d2 + + arriba_draw_fusion: + cytobands: + checksum: 7bd504feefb33fcfc9be0517439a423c + path: ref_data/arriba_v2.3.0/cytobands_hg38_GRCh38_v2.3.0.tsv + type: file + #url: https://figshare.scilifelab.se/ndownloader/files/40928348 + + protein_domains: + checksum: 43c387a784ebeed71b4147076cebf978 + path: ref_data/arriba_v2.3.0/protein_domains_hg38_GRCh38_v2.3.0.gff3 + type: file + #url: https://figshare.scilifelab.se/ndownloader/files/40928354 + + bcftools_annotate: + annotation_db: + checksum: aa2468cb145e390a655976f73dd069ad + path: ref_data/GNOMAD/small_exac_common_3.hg38.vcf.gz + type: file + url: https://figshare.com/ndownloader/files/44326148?private_link=7084cf61820c148a23d2 + + bwa: + amb: + checksum: 04c08086272e0a86043cc51148ece9ef + path: ref_data/GRCh38_p14/homo_sapiens.fasta.amb + type: file + url: https://figshare.com/ndownloader/files/44326166?private_link=7084cf61820c148a23d2 + ann: + checksum: 07b88ee3a7631805de435e4f5b0354c1 + path: ref_data/GRCh38_p14/homo_sapiens.fasta.ann + type: file + url: https://figshare.com/ndownloader/files/44326163?private_link=7084cf61820c148a23d2 + bwt: + checksum: d2c37eb4a95b93065cc47959a456e59e + path: ref_data/GRCh38_p14/homo_sapiens.fasta.bwt + type: file + url: https://figshare.com/ndownloader/files/44326175?private_link=7084cf61820c148a23d2 + pac: + checksum: 7150c22df742fa77e6810aa7a55fc99a + path: ref_data/GRCh38_p14/homo_sapiens.fasta.pac + type: file + url: https://figshare.com/ndownloader/files/44326169?private_link=7084cf61820c148a23d2 + sa: + checksum: 3548426aa7ecaef1e724f7ea52a80a1d + path: ref_data/GRCh38_p14/homo_sapiens.fasta.sa + type: file + url: https://figshare.com/ndownloader/files/44326172?private_link=7084cf61820c148a23d2 + + filter_fuseq_wes: + gtf: + checksum: 9a477533e8e6c47a854a01ccd04b1580 + path: ref_data/refGene/hg38.refGene.gtf + type: file + url: https://figshare.com/ndownloader/files/44406203?private_link=7084cf61820c148a23d2 + + fuseq_wes: + reference: + type: folder + compressed_checksum: 32824ce070546f51888077ab1999061d + path: ref_data/fuseq_wes + content_checksum: + Mitelman_fusiondb.RData: e4fbf81b5b02b9fe201161d324405822 + UCSC_hg38_wes_contigSize3000_bigLen130000_r100.json: 51e501095ddf5dbf276d4d322580430f + UCSC_hg38_wes_contigSize3000_bigLen130000_r100.sqlite: 42412eaf583c2c6e6f5f2cd0fb11d435 + ensmbl_paralogs_grch38.RData: 746f32f17502d3fdb21e8681960bd5ff + url: https://figshare.com/ndownloader/files/44328401?private_link=7084cf61820c148a23d2 + + gatk_get_pileup_summaries: + sites: + checksum: aa2468cb145e390a655976f73dd069ad + path: ref_data/GNOMAD/small_exac_common_3.hg38.vcf.gz + type: file + url: https://figshare.com/ndownloader/files/44326148?private_link=7084cf61820c148a23d2 + + variants: + checksum: aa2468cb145e390a655976f73dd069ad + path: ref_data/GNOMAD/small_exac_common_3.hg38.vcf.gz + type: file + url: https://figshare.com/ndownloader/files/44326148?private_link=7084cf61820c148a23d2 + + variants_tbi: + checksum: da293001edbcb911a8ba218c6c7a4864 + path: ref_data/GNOMAD/small_exac_common_3.hg38.vcf.gz.tbi + type: file + url: https://figshare.com/ndownloader/files/44326154?private_link=7084cf61820c148a23d2 + + references: + fasta: + checksum: e900e9248ef9d1ea1b03e56b185cc5d7 + path: ref_data/GRCh38_p14/homo_sapiens.fasta + type: file + url: https://figshare.com/ndownloader/files/44326178?private_link=7084cf61820c148a23d2 + + fai: + checksum: 7b0d658ae292f8ee17b371d387dbdc0d + path: ref_data/GRCh38_p14/homo_sapiens.fasta.fai + type: file + url: https://figshare.com/ndownloader/files/44326157?private_link=7084cf61820c148a23d2 + + dict: + checksum: cabb2e8bbbf8ad3ab1f7f5177da20044 + path: ref_data/GRCh38_p14/homo_sapiens.fasta.dict + type: file + url: https://figshare.com/ndownloader/files/44326160?private_link=7084cf61820c148a23d2 + + fusioncatcher: + genome_path: + compressed_checksum: 5006482f5b6b78c99e80330d2d69a239 + path: ref_data/fusioncatcher + type: folder + url: + https://figshare.scilifelab.se/ndownloader/files/42061230: 5f4968cf58a28bfe661ee3d1207259c6 + https://figshare.scilifelab.se/ndownloader/files/42061233: ad677c79617e36f85592b45918a10f21 + https://figshare.scilifelab.se/ndownloader/files/42061242: b4a57d1a48b12e3302fa7d12e6ac6347 + https://figshare.scilifelab.se/ndownloader/files/42061248: 1280e3204b6990b825c762ac14e4446a + content_checksum: + human_v102/ucsc_genes_header.txt : 9aa055ae6c632068ddc0f4c60ad9c82f + human_v102/synonyms.txt : dbaea5a7e374e110b4fbb57c2bea3063 + human_v102/exons_header.txt : 5bdb1d9e7484f7f9ac4666545ad41088 + human_v102/shield_against_pseudo-genes.txt : ae05c5a3a1fc94c8d78442e5f539a47d + human_v102/cacg.txt : 6b642c538dca74f9a8e52fb0e853af46 + human_v102/exons_removed.txt : b1761c5f09839ffe66c7729fa848a93b + human_v102/ucsc_fully_overlapping_genes.txt : 90550e334897c4bdad47f3b206783f0e + human_v102/readthroughs.txt : c99203b70603eadac7c8b59f02fb96eb + human_v102/oncokb.txt : 9ab9283758f4b67c0135386117dc535a + human_v102/shielded_reads_similarity.bed : 21643307cb75aed67b1c2c512e52514a + human_v102/mitelman.txt : 0d18ea2267c14b267f1c17954af8268e + human_v102/dgd.txt : 7b081aa70fc08f8d6e4f74d42e9d1a1c + human_v102/genes.txt : 009cf9e1e7866e058bad3226b05b2198 + human_v102/ccle.txt : 9b221f45420fd407e63d8a18473e68f1 + human_v102/non-tumor_cells.txt : 91b50627ee2535d89790a32f73d81f6e + human_v102/descriptions.txt : 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human_v102/exons.fa : cdfa70e1d09ac6f1178b75b7c00a217b + human_v102/snrnas.txt : 8c8e3a8b8718ff13316eae1851aa1da9 + human_v102/custom_transcripts_mark.txt : 0d168c62fd8d2a18dd2ab3a35a48c64d + human_v102/ccle3.txt : a1fce78904317b37801e716cc60b29d8 + human_v102/ensembl_overlapping_genes.txt : ca6ecbfcbedc02b8e64de197ca97ae75 + human_v102/snornas.txt : f33c5eebb4af148627002d922d7a6e9a + human_v102/biotypes.txt : c41bedcbfb6ff273ce170a99e1e217fc + human_v102/transcripts.txt : 189434df13c3fe68b5857b642b8aea12 + human_v102/banned.txt : 4e17fd595314c65bfcf517d54c4db435 + human_v102/chimerdb4pub.txt : 9ce8202c20a8c2b40902b9c49f2b40d6 + human_v102/shield_against_pseudo-genes_not-found.txt : d41d8cd98f00b204e9800998ecf8427e + human_v102/transcripts.fa : f03092994ec073b7cdfe2bba23ccef2a + human_v102/ensembl_same_strand_overlapping_genes.txt : 82946d973acf0ced9056f84eaa6460a2 + human_v102/tcga-normal.txt : 98a1a7a572f1970b08e5257b97c99cde + human_v102/known.txt : d404bff212c3bba70e647073e37212fe 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b23ef9e0270d1da8c5ce8a434ae57fc2 + homo_sapiens_refseq/105_GRCh38/CHR_HG2213_PATCH/48000001-49000000_reg.gz: 990c46bbb7baea8ad847731a37620bec + homo_sapiens_refseq/105_GRCh38/CHR_HG2213_PATCH/48000001-49000000.gz: 0d1d0221d28c3d3570bec73e841dd916 + homo_sapiens_refseq/105_GRCh38/CHR_HG2213_PATCH/all_vars.gz.csi: 6f1ac4c9e33f41796c2c6b81f38ce5b9 + url: https://figshare.com/ndownloader/files/44484626?private_link=7084cf61820c148a23d2 + + From d3e6ea39168aeb56f192d7358a858e0d2bedf3de Mon Sep 17 00:00:00 2001 From: Patrik Smeds Date: Fri, 16 Feb 2024 10:52:19 +0100 Subject: [PATCH 02/40] minor fixes --- config/references/design_files.hg38.yaml | 6 +++--- config/references/references.hg38.yaml | 7 +++++++ 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/config/references/design_files.hg38.yaml b/config/references/design_files.hg38.yaml index 4e44c944..ab332444 100644 --- a/config/references/design_files.hg38.yaml +++ b/config/references/design_files.hg38.yaml @@ -162,10 +162,10 @@ url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed design_intervals: - checksum: 509c6f79e136b8c3de8dbe5b63c29fb0 - path: GMS560/design//pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.interval_list + checksum: 86a073346c27a5c7c5034f82b79ed65c + path: GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.interval_list type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design//pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.interval_list + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.interval_list design_intervals_gatk_cnv: checksum: 58088e1c88e02f7b0cfd5211eabc01cd diff --git a/config/references/references.hg38.yaml b/config/references/references.hg38.yaml index d23fce29..2565cee6 100644 --- a/config/references/references.hg38.yaml +++ b/config/references/references.hg38.yaml @@ -35,26 +35,31 @@ bwa: amb: checksum: 04c08086272e0a86043cc51148ece9ef + link: ref_data/GRCh38_p14/homo_sapiens.amb path: ref_data/GRCh38_p14/homo_sapiens.fasta.amb type: file url: https://figshare.com/ndownloader/files/44326166?private_link=7084cf61820c148a23d2 ann: checksum: 07b88ee3a7631805de435e4f5b0354c1 + link: ref_data/GRCh38_p14/homo_sapiens.ann path: ref_data/GRCh38_p14/homo_sapiens.fasta.ann type: file url: https://figshare.com/ndownloader/files/44326163?private_link=7084cf61820c148a23d2 bwt: checksum: d2c37eb4a95b93065cc47959a456e59e + link: ref_data/GRCh38_p14/homo_sapiens.bwt path: ref_data/GRCh38_p14/homo_sapiens.fasta.bwt type: file url: https://figshare.com/ndownloader/files/44326175?private_link=7084cf61820c148a23d2 pac: checksum: 7150c22df742fa77e6810aa7a55fc99a + link: ref_data/GRCh38_p14/homo_sapiens.pac path: ref_data/GRCh38_p14/homo_sapiens.fasta.pac type: file url: https://figshare.com/ndownloader/files/44326169?private_link=7084cf61820c148a23d2 sa: checksum: 3548426aa7ecaef1e724f7ea52a80a1d + link: ref_data/GRCh38_p14/homo_sapiens.sa path: ref_data/GRCh38_p14/homo_sapiens.fasta.sa type: file url: https://figshare.com/ndownloader/files/44326172?private_link=7084cf61820c148a23d2 @@ -106,12 +111,14 @@ fai: checksum: 7b0d658ae292f8ee17b371d387dbdc0d + link: ref_data/GRCh38_p14/homo_sapiens.fai path: ref_data/GRCh38_p14/homo_sapiens.fasta.fai type: file url: https://figshare.com/ndownloader/files/44326157?private_link=7084cf61820c148a23d2 dict: checksum: cabb2e8bbbf8ad3ab1f7f5177da20044 + link: ref_data/GRCh38_p14/homo_sapiens.dict path: ref_data/GRCh38_p14/homo_sapiens.fasta.dict type: file url: https://figshare.com/ndownloader/files/44326160?private_link=7084cf61820c148a23d2 From 608d2bc8556c138c87964dfe7eff304b11729509 Mon Sep 17 00:00:00 2001 From: Patrik Smeds Date: Fri, 16 Feb 2024 11:22:34 +0100 Subject: [PATCH 03/40] set file version --- config/references/design_files.hg38.yaml | 48 ++++++++++++------------ 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/config/references/design_files.hg38.yaml b/config/references/design_files.hg38.yaml index ab332444..b5a25c30 100644 --- a/config/references/design_files.hg38.yaml +++ b/config/references/design_files.hg38.yaml @@ -5,61 +5,61 @@ path: GMS560/cnv/cnv_amp_genes_hg38.bed checksum: 51ca611484f5b406edfe79f06e8879ef type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/cnv_amp_genes_hg38.bed + url: 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exon_skipping: design_bed: checksum: 75299f3690fd91d8e42e7db3743896b2 path: GMS560/design/Twist_RNA_Design5.annotated.hg38.bed type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/Twist_RNA_Design5.annotated.hg38.bed + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/Twist_RNA_Design5.annotated.hg38.bed filter_fuseq_wes: gene_white_list: @@ -92,98 +92,98 @@ checksum: 32f3be3365e485092c33e9f0997968c1 path: GMS560/cnv/gnomad_SNP_0.001_target.annotated.hg38.interval_list type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/gnomad_SNP_0.001_target.annotated.hg38.interval_list + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/gnomad_SNP_0.001_target.annotated.hg38.interval_list hotspot_annotation: hotspots: checksum: 08c574ec13984188c8e4d2c80c14d2e3 path: 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GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed.gz.tbi type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed.gz.tbi + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed.gz.tbi purecn: intervals: checksum: af529c0ece5fe201de4d507000564ff7 path: GMS560/purecn/targets_twist-gms-st_hg38_25000_intervals.txt type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/targets_twist-gms-st_hg38_25000_intervals.txt + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/targets_twist-gms-st_hg38_25000_intervals.txt purecn_coverage: intervals: checksum: af529c0ece5fe201de4d507000564ff7 path: GMS560/purecn/targets_twist-gms-st_hg38_25000_intervals.txt type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/cnv/targets_twist-gms-st_hg38_25000_intervals.txt + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/targets_twist-gms-st_hg38_25000_intervals.txt report_fusions: annotation_bed: checksum: af529c0ece5fe201de4d507000564ff7 path: GMS560/design/Twist_RNA_fusionpartners_hg38.bed type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/rna_fusion/Twist_RNA_fusionpartners.bed + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/rna_fusion/Twist_RNA_fusionpartners.bed fp_fusions: checksum: eca1c1cf1f1e068cbdada20bdb75c392 path: GMS560/rna_fusion/filter_rna_fusions_20231024.txt type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/rna_fusion/filter_rna_fusions_20231024.txt + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/rna_fusion/filter_rna_fusions_20231024.txt references: design_bed: checksum: ad95a96bfb3416ce6d2aadf6e3df207c path: GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed design_intervals: checksum: 86a073346c27a5c7c5034f82b79ed65c path: GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.interval_list type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.interval_list + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.interval_list design_intervals_gatk_cnv: checksum: 58088e1c88e02f7b0cfd5211eabc01cd path: GMS560/design/gatk.design.hg38.preprocessed.interval_list type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/gatk.design.hg38.preprocessed.interval_list + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/gatk.design.hg38.preprocessed.interval_list design_bed_rna: checksum: ad95a96bfb3416ce6d2aadf6e3df207c path: GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed design_intervals_rna: checksum: 2d05715acc2a54f11e8c2ead3126d76e path: GMS560/design/Twist_RNA_Design5.annotated.hg38.interval_list type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/main/design/Twist_RNA_Design5.annotated.hg38.interval_list + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/design/Twist_RNA_Design5.annotated.hg38.interval_list tmb: filter_genes: From d704c7f7f32bc11e5211d54384c2238c216d1952 Mon Sep 17 00:00:00 2001 From: Patrik Smeds Date: Fri, 16 Feb 2024 11:40:27 +0100 Subject: [PATCH 04/40] fix checksum --- config/references/design_files.hg38.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/config/references/design_files.hg38.yaml b/config/references/design_files.hg38.yaml index b5a25c30..69c0318f 100644 --- a/config/references/design_files.hg38.yaml +++ b/config/references/design_files.hg38.yaml @@ -129,14 +129,14 @@ purecn: intervals: - checksum: af529c0ece5fe201de4d507000564ff7 + checksum: 868c8991360482315f820ae822108965 path: GMS560/purecn/targets_twist-gms-st_hg38_25000_intervals.txt type: file url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/targets_twist-gms-st_hg38_25000_intervals.txt purecn_coverage: intervals: - checksum: af529c0ece5fe201de4d507000564ff7 + checksum: 868c8991360482315f820ae822108965 path: GMS560/purecn/targets_twist-gms-st_hg38_25000_intervals.txt type: file url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/targets_twist-gms-st_hg38_25000_intervals.txt From 1fddcad56507c1e7ba766de4fadc2318a3e8d508 Mon Sep 17 00:00:00 2001 From: Patrik Smeds Date: Wed, 21 Feb 2024 13:43:18 +0100 Subject: [PATCH 05/40] Update references.hg19.yaml --- config/references/references.hg19.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/references/references.hg19.yaml b/config/references/references.hg19.yaml index 07a07e2d..3468f8c7 100644 --- a/config/references/references.hg19.yaml +++ b/config/references/references.hg19.yaml @@ -6,7 +6,7 @@ path: ref_data/arriba_v2.3.0 type: folder content_checksum: - : ca7b0b42ec2498814a5c408a5477e052 + blacklist_hg19_hs37d5_GRCh37_v2.3.0.tsv.gz: ca7b0b42ec2498814a5c408a5477e052 cytobands_hg19_hs37d5_GRCh37_v2.3.0.tsv: 9333eaa96c56fa22624ab432b8391b2b known_fusions_hg19_hs37d5_GRCh37_v2.3.0.tsv.gz: 2f063a0065c1c88d86c859b924d8d590 protein_domains_hg19_hs37d5_GRCh37_v2.3.0.gff3: b5bc63c70c9eb08c71528ee8b0186901 From fabe8ae4c0203f81f24102a3bbce12827a8de825 Mon Sep 17 00:00:00 2001 From: Patrik Smeds Date: Wed, 21 Feb 2024 13:44:10 +0100 Subject: [PATCH 06/40] Update requirements.txt --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 79df631e..3fe98673 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ -hydra-genetics==1.11.1 +hydra-genetics==1.12.0 pandas>=1.3.1 snakemake==7.18.0 singularity==3.0.0 From a9dea4efea6fe38490bbd3b656624735a8f07341 Mon Sep 17 00:00:00 2001 From: jonca79 <54137490+jonca79@users.noreply.github.com> Date: Fri, 22 Mar 2024 12:53:27 +0100 Subject: [PATCH 07/40] fix: add implied msi configuration from module to config --- config/config.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/config/config.yaml b/config/config.yaml index 8e4a7739..e59c8b9c 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -199,6 +199,7 @@ mosdepth_bed: msisensor_pro: container: "docker://hydragenetics/msisensor_pro:1.1.a" + extra: "-c 50" multiqc: container: "docker://hydragenetics/multiqc:1.11" From 1d9a027bc274a475bd054f5f180c5ada3fe8a1f1 Mon Sep 17 00:00:00 2001 From: jonca79 <54137490+jonca79@users.noreply.github.com> Date: Tue, 9 Apr 2024 11:20:38 +0200 Subject: [PATCH 08/40] feat: do not merge regions that are not identical Some GATK CNV results are missing from the table as they where merged with CNVkit results. This will mitigate this. --- config/config.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/config/config.yaml b/config/config.yaml index 8e4a7739..1c033346 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -316,6 +316,7 @@ svdb_merge: cnv_caller: - cnvkit - gatk + overlap: 1 #Just merge the two vcf-files without merging regions extra: "--pass_only" #Just merge the two vcf-files without merging regions svdb_query: From 75490367490628b403907cf1e5126483a1435fa2 Mon Sep 17 00:00:00 2001 From: jonca79 <54137490+jonca79@users.noreply.github.com> Date: Wed, 10 Apr 2024 11:53:50 +0200 Subject: [PATCH 09/40] fix: add "_" to regexp so that indels are reported correctly --- config/reports/hotspot_report.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/reports/hotspot_report.yaml b/config/reports/hotspot_report.yaml index 632e7700..a7fb1820 100644 --- a/config/reports/hotspot_report.yaml +++ b/config/reports/hotspot_report.yaml @@ -33,7 +33,7 @@ columns: AA_change: from: 'vep' field: 'HGVSp' - extract_regex: ':p.([A-Za-z0-9]+)' + extract_regex: ':p.([A-Za-z0-9_]+)' order: 7 CDS_change: from: 'vep' From ccbe735010ffb680a5d5ae05a1d848453916ee8d Mon Sep 17 00:00:00 2001 From: jonca79 Date: Mon, 15 Apr 2024 13:23:21 +0200 Subject: [PATCH 10/40] feat: added chromosome arm support to rule --- .tests/integration/config/config.yaml | 9 ++++++- .../reference/chromosome_arm_size.tsv | 25 +++++++++++++++++++ config/config.yaml | 5 +++- workflow/rules/cnv_tsv_report.smk | 23 ++++++++++------- 4 files changed, 51 insertions(+), 11 deletions(-) create mode 100644 .tests/integration/reference/chromosome_arm_size.tsv diff --git a/.tests/integration/config/config.yaml b/.tests/integration/config/config.yaml index b81f8e47..d6ad2859 100644 --- a/.tests/integration/config/config.yaml +++ b/.tests/integration/config/config.yaml @@ -41,7 +41,6 @@ call_small_cnv_deletions: call_small_cnv_amplifications: regions_file: "DATA/cnv_amplification_genes.tsv" - cnvkit_batch: normal_reference: "DATA/design.PoN.cnn" method: "hybrid" @@ -52,6 +51,14 @@ cnvkit_batch_hrd: cnv_html_report: template_dir: "../../config/reports/cnv_report_template" +cnv_tsv_report: + amp_cn_limit: 6.0 + chrom_arm_size: "reference/chromosome_arm_size.tsv" + del_1p19q_cn_limit: 1.4 + del_1p19q_chr_arm_fraction: 0.3 + chr_arm_fraction: 0.5 + del_chr_arm_cn_limit: 1.4 + amp_chr_arm_cn_limit: 2.5 exon_skipping: design_bed: "reference/Twist_RNA_Design5.annotated.bed" diff --git a/.tests/integration/reference/chromosome_arm_size.tsv b/.tests/integration/reference/chromosome_arm_size.tsv new file mode 100644 index 00000000..970d7dd3 --- /dev/null +++ b/.tests/integration/reference/chromosome_arm_size.tsv @@ -0,0 +1,25 @@ +chromosome p q +chr1 125000000 124250621 +chr2 93300000 149899373 +chr3 91000000 107022430 +chr4 50400000 140754276 +chr5 48400000 132515260 +chr6 61000000 110115067 +chr7 59900000 99238663 +chr8 45600000 100764022 +chr9 49000000 92213431 +chr10 40200000 95334747 +chr11 53700000 81306516 +chr12 35800000 98051895 +chr13 17900000 97269878 +chr14 17600000 89749540 +chr15 19000000 83531392 +chr16 36600000 53754753 +chr17 24000000 57195210 +chr18 17200000 60877248 +chr19 26500000 32628983 +chr20 27500000 35525520 +chr21 13200000 34929895 +chr22 14700000 36604566 +chrX 60600000 94670560 +chrY 12500000 46873566 diff --git a/config/config.yaml b/config/config.yaml index 8e4a7739..1c73a31a 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -83,9 +83,12 @@ cnv_html_report: cnv_tsv_report: amp_cn_limit: 6.0 + chrom_arm_size: "{{PROJECT_DESIGN_DATA}}/GMS560/design/chromosome_arm_size.tsv" del_1p19q_cn_limit: 1.4 del_1p19q_chr_arm_fraction: 0.3 - + chr_arm_fraction: 0.5 + del_chr_arm_cn_limit: 1.4 + amp_chr_arm_cn_limit: 2.5 fastp_pe: container: "docker://hydragenetics/fastp:0.20.1" diff --git a/workflow/rules/cnv_tsv_report.smk b/workflow/rules/cnv_tsv_report.smk index 1ed8ab15..ecbf86df 100644 --- a/workflow/rules/cnv_tsv_report.smk +++ b/workflow/rules/cnv_tsv_report.smk @@ -6,24 +6,29 @@ __license__ = "GPL-3" rule cnv_tsv_report: input: - vcfs=[ - "cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.cnv_amp_genes.filter.cnv_hard_filter_amp.vcf", - "cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.{tag}.filter.cnv_hard_filter_loh.vcf", - ], + amplifications="cnv_sv/call_small_cnv_amplifications/{sample}_{type}.amplifications.tsv", + chrom_arm_size=config.get("cnv_tsv_report", {}).get("chrom_arm_size", ""), + deletions="cnv_sv/call_small_cnv_deletions/{sample}_{type}.deletions.tsv", org_vcfs=[ "cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.cnv_amp_genes.vcf", "cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.{tag}.vcf", ], - deletions="cnv_sv/call_small_cnv_deletions/{sample}_{type}.deletions.tsv", - amplifications="cnv_sv/call_small_cnv_amplifications/{sample}_{type}.amplifications.tsv", tc_file=get_tc_file, + vcfs=[ + "cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.cnv_amp_genes.filter.cnv_hard_filter_amp.vcf", + "cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.{tag}.filter.cnv_hard_filter_loh.vcf", + ], output: tsv=temp("cnv_sv/svdb_query/{sample}_{type}.{tc_method}.{tag}.cnv_report.tsv"), tsv_additional_only=temp("cnv_sv/svdb_query/{sample}_{type}.{tc_method}.{tag}.cnv_additional_variants_only.tsv"), + tsv_chrom_arms=temp("cnv_sv/svdb_query/{sample}_{type}.{tc_method}.{tag}.cnv_chromosome_arms.tsv")) params: - call_small_amplifications_cn_limit=config.get("cnv_tsv_report", {}).get("amp_cn_limit", "6"), - del_1p19q_cn_limit=config.get("cnv_tsv_report", {}).get("del_1p19q_cn_limit", "2"), - del_1p19q_chr_arm_fraction=config.get("cnv_tsv_report", {}).get("del_1p19q_chr_arm_fraction", "0"), + call_small_amplifications_cn_limit=config.get("cnv_tsv_report", {}).get("amp_cn_limit", ""), + del_1p19q_cn_limit=config.get("cnv_tsv_report", {}).get("del_1p19q_cn_limit", ""), + del_1p19q_chr_arm_fraction=config.get("cnv_tsv_report", {}).get("del_1p19q_chr_arm_fraction", ""), + chrom_del=config.get("cnv_tsv_report", {}).get("chr_arm_fraction", ""), + chrom_del_cn_limit=config.get("cnv_tsv_report", {}).get("del_chr_arm_cn_limit", ""), + chrom_amp_cn_limit=config.get("cnv_tsv_report", {}).get("amp_chr_arm_cn_limit", ""), tc=get_tc, log: "cnv_sv/svdb_query/{sample}_{type}.{tc_method}.{tag}.cnv_report.tsv.log", From 667d53fe56eb15047ca326a91957bbfdb30065fd Mon Sep 17 00:00:00 2001 From: jonca79 Date: Mon, 15 Apr 2024 14:07:55 +0200 Subject: [PATCH 11/40] feat: added calculation of cnv in chrom arms --- workflow/rules/cnv_tsv_report.smk | 6 +-- workflow/scripts/cnv_report.py | 69 +++++++++++++++++++++++++++---- 2 files changed, 64 insertions(+), 11 deletions(-) diff --git a/workflow/rules/cnv_tsv_report.smk b/workflow/rules/cnv_tsv_report.smk index ecbf86df..a46c877d 100644 --- a/workflow/rules/cnv_tsv_report.smk +++ b/workflow/rules/cnv_tsv_report.smk @@ -26,9 +26,9 @@ rule cnv_tsv_report: call_small_amplifications_cn_limit=config.get("cnv_tsv_report", {}).get("amp_cn_limit", ""), del_1p19q_cn_limit=config.get("cnv_tsv_report", {}).get("del_1p19q_cn_limit", ""), del_1p19q_chr_arm_fraction=config.get("cnv_tsv_report", {}).get("del_1p19q_chr_arm_fraction", ""), - chrom_del=config.get("cnv_tsv_report", {}).get("chr_arm_fraction", ""), - chrom_del_cn_limit=config.get("cnv_tsv_report", {}).get("del_chr_arm_cn_limit", ""), - chrom_amp_cn_limit=config.get("cnv_tsv_report", {}).get("amp_chr_arm_cn_limit", ""), + chr_arm_fraction=config.get("cnv_tsv_report", {}).get("chr_arm_fraction", ""), + del_chr_arm_cn_limit=config.get("cnv_tsv_report", {}).get("del_chr_arm_cn_limit", ""), + amp_chr_arm_cn_limit=config.get("cnv_tsv_report", {}).get("amp_chr_arm_cn_limit", ""), tc=get_tc, log: "cnv_sv/svdb_query/{sample}_{type}.{tc_method}.{tag}.cnv_report.tsv.log", diff --git a/workflow/scripts/cnv_report.py b/workflow/scripts/cnv_report.py index 314b95c4..6cf36f76 100644 --- a/workflow/scripts/cnv_report.py +++ b/workflow/scripts/cnv_report.py @@ -6,9 +6,25 @@ def create_tsv_report( - input_vcfs, input_org_vcfs, input_del, input_amp, amp_cn_limit, - output_txt, out_additional_only, del_1p19q_cn, del_1p19q_chr_arm_fraction, TC + input_vcfs, input_org_vcfs, input_del, input_amp, in_chrom_arm_size, amp_cn_limit, + output_txt, out_additional_only, out_tsv_chrom_arms, del_1p19q_cn, del_1p19q_chr_arm_fraction, + chr_arm_fraction, del_chr_arm_cn_limit, amp_chr_arm_cn_limit, TC ): + + chrom_arm_size = {} + chrom_arm_del = {} + chrom_arm_amp = {} + with open(in_chrom_arm_size) as chrom_arm_size: + chrom_arm_size.next() + for line in chrom_arm_size: + columns = line.strip().split("\t") + chrom = columns[0] + p_size = int(columns[1]) + q_size = int(columns[2]) + chrom_arm_size[chrom] = [[0, p_size, p_size], [p_size, p_size + q_size, q_size]] + chrom_arm_del[chrom] = [0, 0] + chrom_arm_amp[chrom] = [0, 0] + gene_all_dict = {} nr_writes = 0 log.info(f"Opening output tsv file: {output_txt}") @@ -37,6 +53,7 @@ def create_tsv_report( chr = variant.chrom start = variant.pos end = variant.pos + int(utils.get_annotation_data_info(variant, "SVLEN")) - 1 + size = end - start + 1 callers = utils.get_annotation_data_info(variant, "CALLER") cn = utils.get_annotation_data_info(variant, "CORR_CN") AF = utils.get_annotation_data_info(variant, "Twist_AF") @@ -44,14 +61,24 @@ def create_tsv_report( AF = 0.0 if cn < del_1p19q_cn and chr == "chr1" and start >= del_1p19q["1p"][0] and start <= del_1p19q["1p"][1]: if callers == "cnvkit": - del_1p19q["1p_cnvkit"] += end - start + 1 + del_1p19q["1p_cnvkit"] += size elif callers == "gatk": - del_1p19q["1p_gatkcnv"] += end - start + 1 + del_1p19q["1p_gatkcnv"] += size if cn < del_1p19q_cn and chr == "chr19" and start >= del_1p19q["19q"][0] and start <= del_1p19q["19q"][1]: if callers == "cnvkit": - del_1p19q["19q_cnvkit"] += end - start + 1 + del_1p19q["19q_cnvkit"] += size elif callers == "gatk": - del_1p19q["19q_gatkcnv"] += end - start + 1 + del_1p19q["19q_gatkcnv"] += size + if cn < del_chr_arm_cn_limit and caller == "cnvkit": + if start >= chrom_arm_size[chr][0][0] and start <= chrom_arm_size[chr][0][1]: + chrom_arm_del[chr][0] += size + else: + chrom_arm_del[chr][1] += size + if cn > amp_chr_arm_cn_limit and caller == "cnvkit": + if start >= chrom_arm_size[chr][0][0] and start <= chrom_arm_size[chr][0][1]: + chrom_arm_amp[chr][0] += size + else: + chrom_arm_amp[chr][1] += size if genes is not None: for gene in genes.split(","): if gene not in gene_all_dict: @@ -73,10 +100,10 @@ def create_tsv_report( nr_writes += 1 if (del_1p19q["1p_gatkcnv"] / del_1p19q["1p"][2] > del_1p19q_chr_arm_fraction and del_1p19q["19q_gatkcnv"] / del_1p19q["19q"][2] > del_1p19q_chr_arm_fraction): - if nr_writes < 2: + if nr_writes < 3: writer.write(f"\n{samples}\t1p19q\tNA\tNA\tgatk_cnv\tNA\tNA") out_additional_only.write(f"\n{samples}\t1p19q\tNA\tNA\tgatk_cnv\tNA\tNA") - nr_writes += 1 + nr_writes += 1 for input_vcf in input_vcfs: gene_variant_dict = {} @@ -163,16 +190,37 @@ def create_tsv_report( writer.write(f"\n{sample_name}\t{gene}\t{chr}\t{start}-{end}\t{callers}\t{AF}\t{ccn:.2f}") out_additional_only.write(f"\n{sample_name}\t{gene}\t{chr}\t{start}-{end}\t{callers}\t{AF}\t{ccn:.2f}") + with open(out_tsv_chrom_arms, "w") as writer: + writer.write("sample\tchrom\tarm\tcaller\ttype\tfraction") + for chrom in chrom_arm_del: + if chrom_arm_del[chrom][0] / chrom_arm_size[chrom][0] > chr_arm_fraction: + writer.write(f"\n{chrom}\tp\tcnvkit\tdeletion\t{chrom_arm_del[chrom][0] * 100 / chrom_arm_size[chrom][0]}%") + if chrom_arm_del[chrom][1] / chrom_arm_size[chrom][1] > chr_arm_fraction: + writer.write(f"\n{chrom}\tp\tcnvkit\tdeletion\t{chrom_arm_del[chrom][1] * 100 / chrom_arm_size[chrom][1]}%") + if chrom_arm_amp[chrom][0] / chrom_arm_size[chrom][0] > chr_arm_fraction: + writer.write(f"\n{chrom}\tp\tcnvkit\tduplication\t{chrom_arm_amp[chrom][0] * 100 / chrom_arm_size[chrom][0]}%") + if chrom_arm_amp[chrom][1] / chrom_arm_size[chrom][1] > chr_arm_fraction: + writer.write(f"\n{chrom}\tp\tcnvkit\tduplication\t{chrom_arm_amp[chrom][1] * 100 / chrom_arm_size[chrom][1]}%") + + + + + if __name__ == "__main__": in_vcfs = snakemake.input.vcfs in_org_vcfs = snakemake.input.org_vcfs in_del = snakemake.input.deletions in_amp = snakemake.input.amplifications + in_chrom_arm_size = snakemake.input.chrom_arm_size amp_cn_limit = snakemake.params.call_small_amplifications_cn_limit out_tsv = snakemake.output.tsv + out_tsv_chrom_arms = snakemake.output.tsv_chrom_arms del_1p19q_cn = snakemake.params.del_1p19q_cn_limit del_1p19q_chr_arm_fraction = snakemake.params.del_1p19q_chr_arm_fraction + chr_arm_fraction = snakemake.params.chr_arm_fraction + del_chr_arm_cn_limit = snakemake.params.del_chr_arm_cn_limit + amp_chr_arm_cn_limit = snakemake.params.amp_chr_arm_cn_limit TC = float(snakemake.params.tc) with open(snakemake.output.tsv_additional_only, "w") as out_additional_only: create_tsv_report( @@ -180,10 +228,15 @@ def create_tsv_report( in_org_vcfs, in_del, in_amp, + in_chrom_arm_size, amp_cn_limit, out_tsv, out_additional_only, + out_tsv_chrom_arms, del_1p19q_cn, del_1p19q_chr_arm_fraction, + chr_arm_fraction, + del_chr_arm_cn_limit, + amp_chr_arm_cn_limit, TC, ) From b1c9bfea96a960aa0e048753c27fa9858e5c625f Mon Sep 17 00:00:00 2001 From: jonca79 Date: Mon, 15 Apr 2024 14:26:04 +0200 Subject: [PATCH 12/40] docs: added schema --- workflow/schemas/config.schema.yaml | 13 +++++++++++++ workflow/schemas/rules.schema.yaml | 19 +++++++++++++++++-- workflow/scripts/cnv_report.py | 9 ++------- 3 files changed, 32 insertions(+), 9 deletions(-) diff --git a/workflow/schemas/config.schema.yaml b/workflow/schemas/config.schema.yaml index 5cb8d998..33bfdb37 100644 --- a/workflow/schemas/config.schema.yaml +++ b/workflow/schemas/config.schema.yaml @@ -98,15 +98,28 @@ properties: cnv_tsv_report: type: object properties: + amp_chr_arm_cn_limit: + type: number + description: Lower limit of copy number to be included in calculation of chr_arm_fraction for duplications container: type: string description: name or path to docker/singularity container + call_small_amplifications_cn_limit: + type: number + description: Upper limit of copy number to be reported as a small amplification. + chr_arm_fraction: + type: number + description: Fraction of the chromosome arms that needs to be deleted del_1p19q_cn_limit: type: number description: Upper limit of copy number to be included in calculation of del_1p19q_chr_arm_fraction del_1p19q_chr_arm_fraction: type: number description: Fraction of the chromosome arms that needs to be deleted + del_chr_arm_cn_limit: + type: number + description: Upper limit of copy number to be included in calculation of chr_arm_fraction for deletions + cnvkit_batch: type: object diff --git a/workflow/schemas/rules.schema.yaml b/workflow/schemas/rules.schema.yaml index 53aa9db7..b6b4b0df 100644 --- a/workflow/schemas/rules.schema.yaml +++ b/workflow/schemas/rules.schema.yaml @@ -82,12 +82,21 @@ properties: type: object description: list of inputs properties: - vcfs: + amplifications: type: string - description: Filtered vcf-files with merged calls from CNVkit and GATK CNV + description: File with small CNV amplifications generated by call_small_cnv_amplifications + deletions: + type: string + description: File with small CNV amplifications generated by call_small_cnv_deletions org_vcfs: type: string description: Unfiltered vcf-files with merged calls from CNVkit and GATK CNV + tc_file: + type: string + description: Tumor content of sample + vcfs: + type: string + description: Filtered vcf-files with merged calls from CNVkit and GATK CNV output: type: object description: list of outputs @@ -95,6 +104,12 @@ properties: tsv: type: string description: A CNV report in excel friendly format + tsv_additional_only: + type: string + description: File where only additional CNVs are reported. Used for extra table in CNV-html report. + tsv_chrom_arms: + type: string + description: File where large CNVs are reported. Used for extra table in CNV-html report. exon_skipping: type: object diff --git a/workflow/scripts/cnv_report.py b/workflow/scripts/cnv_report.py index 6cf36f76..dcb1cf79 100644 --- a/workflow/scripts/cnv_report.py +++ b/workflow/scripts/cnv_report.py @@ -7,10 +7,9 @@ def create_tsv_report( input_vcfs, input_org_vcfs, input_del, input_amp, in_chrom_arm_size, amp_cn_limit, - output_txt, out_additional_only, out_tsv_chrom_arms, del_1p19q_cn, del_1p19q_chr_arm_fraction, + output_txt, out_additional_only, out_tsv_chrom_arms, del_1p19q_cn, del_1p19q_chr_arm_fraction, chr_arm_fraction, del_chr_arm_cn_limit, amp_chr_arm_cn_limit, TC ): - chrom_arm_size = {} chrom_arm_del = {} chrom_arm_amp = {} @@ -103,7 +102,7 @@ def create_tsv_report( if nr_writes < 3: writer.write(f"\n{samples}\t1p19q\tNA\tNA\tgatk_cnv\tNA\tNA") out_additional_only.write(f"\n{samples}\t1p19q\tNA\tNA\tgatk_cnv\tNA\tNA") - nr_writes += 1 + nr_writes += 1 for input_vcf in input_vcfs: gene_variant_dict = {} @@ -201,10 +200,6 @@ def create_tsv_report( writer.write(f"\n{chrom}\tp\tcnvkit\tduplication\t{chrom_arm_amp[chrom][0] * 100 / chrom_arm_size[chrom][0]}%") if chrom_arm_amp[chrom][1] / chrom_arm_size[chrom][1] > chr_arm_fraction: writer.write(f"\n{chrom}\tp\tcnvkit\tduplication\t{chrom_arm_amp[chrom][1] * 100 / chrom_arm_size[chrom][1]}%") - - - - if __name__ == "__main__": From 9a25cdc0843f188fe1725231740db65d21181d0e Mon Sep 17 00:00:00 2001 From: jonca79 Date: Tue, 16 Apr 2024 13:21:13 +0200 Subject: [PATCH 13/40] feat: added warnings for baseline and polyploidy --- workflow/scripts/cnv_report.py | 63 +++++++++++++++++++++++++++------- 1 file changed, 51 insertions(+), 12 deletions(-) diff --git a/workflow/scripts/cnv_report.py b/workflow/scripts/cnv_report.py index dcb1cf79..ffd43235 100644 --- a/workflow/scripts/cnv_report.py +++ b/workflow/scripts/cnv_report.py @@ -13,6 +13,9 @@ def create_tsv_report( chrom_arm_size = {} chrom_arm_del = {} chrom_arm_amp = {} + baseline = [0, 0] + polyploidy = 0 + genome_size = 0 with open(in_chrom_arm_size) as chrom_arm_size: chrom_arm_size.next() for line in chrom_arm_size: @@ -23,6 +26,7 @@ def create_tsv_report( chrom_arm_size[chrom] = [[0, p_size, p_size], [p_size, p_size + q_size, q_size]] chrom_arm_del[chrom] = [0, 0] chrom_arm_amp[chrom] = [0, 0] + genome_size += p_size + q_size gene_all_dict = {} nr_writes = 0 @@ -31,6 +35,7 @@ def create_tsv_report( with open(output_txt, "w") as writer: writer.write("sample\tgene(s)\tchrom\tregion\tcallers\tfreq_in_db\tcopy_number") out_additional_only.write("sample\tgene(s)\tchrom\tregion\tcallers\tfreq_in_db\tcopy_number") + file1 = True for input_org_vcf in input_org_vcfs: del_1p19q = { "1p_cnvkit": 0, "19q_cnvkit": 0, "1p_gatkcnv": 0, "19q_gatkcnv": 0, @@ -56,8 +61,12 @@ def create_tsv_report( callers = utils.get_annotation_data_info(variant, "CALLER") cn = utils.get_annotation_data_info(variant, "CORR_CN") AF = utils.get_annotation_data_info(variant, "Twist_AF") + BAF = utils.get_annotation_data_info(variant, "BAF") + if BAF != "": + BAF = float(BAF) if AF is None: AF = 0.0 + # 1p19q deletion if cn < del_1p19q_cn and chr == "chr1" and start >= del_1p19q["1p"][0] and start <= del_1p19q["1p"][1]: if callers == "cnvkit": del_1p19q["1p_cnvkit"] += size @@ -68,16 +77,35 @@ def create_tsv_report( del_1p19q["19q_cnvkit"] += size elif callers == "gatk": del_1p19q["19q_gatkcnv"] += size - if cn < del_chr_arm_cn_limit and caller == "cnvkit": - if start >= chrom_arm_size[chr][0][0] and start <= chrom_arm_size[chr][0][1]: - chrom_arm_del[chr][0] += size - else: - chrom_arm_del[chr][1] += size - if cn > amp_chr_arm_cn_limit and caller == "cnvkit": - if start >= chrom_arm_size[chr][0][0] and start <= chrom_arm_size[chr][0][1]: - chrom_arm_amp[chr][0] += size - else: - chrom_arm_amp[chr][1] += size + # Large chromosome CNV + if file1: + if cn < del_chr_arm_cn_limit and caller == "cnvkit": + if start >= chrom_arm_size[chr][0][0] and start <= chrom_arm_size[chr][0][1]: + chrom_arm_del[chr][0] += size + else: + chrom_arm_del[chr][1] += size + if cn > amp_chr_arm_cn_limit and caller == "cnvkit": + if start >= chrom_arm_size[chr][0][0] and start <= chrom_arm_size[chr][0][1]: + chrom_arm_amp[chr][0] += size + else: + chrom_arm_amp[chr][1] += size + # Baseline check + if file1: + if cn > 1.8 and cn < 2.2: + if caller == "cnvkit": + baseline[0] += size + else: + baseline[1] += size + # Poliploidy check + if file1: + if caller == "cnvkit": + if cn > 1.8 and cn < 2.2 and BAF != "" and (BAF < 0.3 or BAF > 0.7): + polyploidy += size + elif cn > 2.5 and BAF != "" and (BAF > 0.4 and BAF < 0.6): + polyploidy += size + elif cn < 1.4 and BAF != "" and (BAF > 0.4 and BAF < 0.6): + polyploidy += size + if genes is not None: for gene in genes.split(","): if gene not in gene_all_dict: @@ -99,11 +127,13 @@ def create_tsv_report( nr_writes += 1 if (del_1p19q["1p_gatkcnv"] / del_1p19q["1p"][2] > del_1p19q_chr_arm_fraction and del_1p19q["19q_gatkcnv"] / del_1p19q["19q"][2] > del_1p19q_chr_arm_fraction): - if nr_writes < 3: + if nr_writes < 2: writer.write(f"\n{samples}\t1p19q\tNA\tNA\tgatk_cnv\tNA\tNA") out_additional_only.write(f"\n{samples}\t1p19q\tNA\tNA\tgatk_cnv\tNA\tNA") nr_writes += 1 + file1 = False + for input_vcf in input_vcfs: gene_variant_dict = {} log.info(f"Opening vcf file: {input_vcf}") @@ -190,7 +220,16 @@ def create_tsv_report( out_additional_only.write(f"\n{sample_name}\t{gene}\t{chr}\t{start}-{end}\t{callers}\t{AF}\t{ccn:.2f}") with open(out_tsv_chrom_arms, "w") as writer: - writer.write("sample\tchrom\tarm\tcaller\ttype\tfraction") + print(baseline[0] / genome_size) + print(baseline[1] / genome_size) + print(polyploidy / genome_size) + writer.write("chrom\tarm\tcaller\ttype\tfraction") + if baseline[0] / genome_size < 0.2: + writer.write(f"\nWarning: baseline of GATK CNV might not ne correct!") + if baseline[1] / genome_size < 0.2: + writer.write(f"\nWarning: baseline of CNVkit might not ne correct!") + if polyploidy / genome_size > 0.5: + writer.write(f"\nWarning: potential polyploidy detected!") for chrom in chrom_arm_del: if chrom_arm_del[chrom][0] / chrom_arm_size[chrom][0] > chr_arm_fraction: writer.write(f"\n{chrom}\tp\tcnvkit\tdeletion\t{chrom_arm_del[chrom][0] * 100 / chrom_arm_size[chrom][0]}%") From e681fee009e69cd73b8e78c05e5aa9fc6cfddd27 Mon Sep 17 00:00:00 2001 From: jonca79 Date: Tue, 16 Apr 2024 13:26:59 +0200 Subject: [PATCH 14/40] fix: bugfix --- workflow/rules/cnv_tsv_report.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/cnv_tsv_report.smk b/workflow/rules/cnv_tsv_report.smk index a46c877d..eaf04734 100644 --- a/workflow/rules/cnv_tsv_report.smk +++ b/workflow/rules/cnv_tsv_report.smk @@ -21,7 +21,7 @@ rule cnv_tsv_report: output: tsv=temp("cnv_sv/svdb_query/{sample}_{type}.{tc_method}.{tag}.cnv_report.tsv"), tsv_additional_only=temp("cnv_sv/svdb_query/{sample}_{type}.{tc_method}.{tag}.cnv_additional_variants_only.tsv"), - tsv_chrom_arms=temp("cnv_sv/svdb_query/{sample}_{type}.{tc_method}.{tag}.cnv_chromosome_arms.tsv")) + tsv_chrom_arms=temp("cnv_sv/svdb_query/{sample}_{type}.{tc_method}.{tag}.cnv_chromosome_arms.tsv"), params: call_small_amplifications_cn_limit=config.get("cnv_tsv_report", {}).get("amp_cn_limit", ""), del_1p19q_cn_limit=config.get("cnv_tsv_report", {}).get("del_1p19q_cn_limit", ""), From 9a92bf222bfb160804748166d49b3d54c6b646ec Mon Sep 17 00:00:00 2001 From: jonca79 Date: Wed, 17 Apr 2024 14:08:53 +0200 Subject: [PATCH 15/40] feat: added more config variables --- config/config.yaml | 4 ++ workflow/rules/cnv_tsv_report.smk | 10 ++- workflow/scripts/cnv_report.py | 103 +++++++++++++++++------------- 3 files changed, 71 insertions(+), 46 deletions(-) diff --git a/config/config.yaml b/config/config.yaml index 1c73a31a..f5ac72da 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -89,6 +89,10 @@ cnv_tsv_report: chr_arm_fraction: 0.5 del_chr_arm_cn_limit: 1.4 amp_chr_arm_cn_limit: 2.5 + normal_baf_lower_limit: 0.4 + normal_baf_upper_limit: 0.6 + normal_cn_lower_limit: 1.7 + normal_cn_upper_limit: 2.25 fastp_pe: container: "docker://hydragenetics/fastp:0.20.1" diff --git a/workflow/rules/cnv_tsv_report.smk b/workflow/rules/cnv_tsv_report.smk index eaf04734..b8039cb2 100644 --- a/workflow/rules/cnv_tsv_report.smk +++ b/workflow/rules/cnv_tsv_report.smk @@ -23,12 +23,16 @@ rule cnv_tsv_report: tsv_additional_only=temp("cnv_sv/svdb_query/{sample}_{type}.{tc_method}.{tag}.cnv_additional_variants_only.tsv"), tsv_chrom_arms=temp("cnv_sv/svdb_query/{sample}_{type}.{tc_method}.{tag}.cnv_chromosome_arms.tsv"), params: + amp_chr_arm_cn_limit=config.get("cnv_tsv_report", {}).get("amp_chr_arm_cn_limit", ""), call_small_amplifications_cn_limit=config.get("cnv_tsv_report", {}).get("amp_cn_limit", ""), - del_1p19q_cn_limit=config.get("cnv_tsv_report", {}).get("del_1p19q_cn_limit", ""), - del_1p19q_chr_arm_fraction=config.get("cnv_tsv_report", {}).get("del_1p19q_chr_arm_fraction", ""), chr_arm_fraction=config.get("cnv_tsv_report", {}).get("chr_arm_fraction", ""), del_chr_arm_cn_limit=config.get("cnv_tsv_report", {}).get("del_chr_arm_cn_limit", ""), - amp_chr_arm_cn_limit=config.get("cnv_tsv_report", {}).get("amp_chr_arm_cn_limit", ""), + del_1p19q_cn_limit=config.get("cnv_tsv_report", {}).get("del_1p19q_cn_limit", ""), + del_1p19q_chr_arm_fraction=config.get("cnv_tsv_report", {}).get("del_1p19q_chr_arm_fraction", ""), + normal_cn_lower_limit=config.get("cnv_tsv_report", {}).get("normal_cn_lower_limit", ""), + normal_cn_upper_limit=config.get("cnv_tsv_report", {}).get("normal_cn_upper_limit", ""), + normal_baf_lower_limit=config.get("cnv_tsv_report", {}).get("normal_cn_lower_limit", ""), + normal_baf_upper_limit=config.get("cnv_tsv_report", {}).get("normal_cn_upper_limit", ""), tc=get_tc, log: "cnv_sv/svdb_query/{sample}_{type}.{tc_method}.{tag}.cnv_report.tsv.log", diff --git a/workflow/scripts/cnv_report.py b/workflow/scripts/cnv_report.py index ffd43235..52cb9c4e 100644 --- a/workflow/scripts/cnv_report.py +++ b/workflow/scripts/cnv_report.py @@ -8,23 +8,26 @@ def create_tsv_report( input_vcfs, input_org_vcfs, input_del, input_amp, in_chrom_arm_size, amp_cn_limit, output_txt, out_additional_only, out_tsv_chrom_arms, del_1p19q_cn, del_1p19q_chr_arm_fraction, - chr_arm_fraction, del_chr_arm_cn_limit, amp_chr_arm_cn_limit, TC + chr_arm_fraction, del_chr_arm_cn_limit, amp_chr_arm_cn_limit, normal_cn_lower_limit, normal_cn_upper_limit, + normal_baf_lower_limit, normal_baf_upper_limit,TC ): chrom_arm_size = {} chrom_arm_del = {} + chrom_arm_loh = {} chrom_arm_amp = {} baseline = [0, 0] polyploidy = 0 genome_size = 0 - with open(in_chrom_arm_size) as chrom_arm_size: - chrom_arm_size.next() - for line in chrom_arm_size: + with open(in_chrom_arm_size) as chrom_arm_size_file: + next(chrom_arm_size_file) + for line in chrom_arm_size_file: columns = line.strip().split("\t") chrom = columns[0] p_size = int(columns[1]) q_size = int(columns[2]) chrom_arm_size[chrom] = [[0, p_size, p_size], [p_size, p_size + q_size, q_size]] chrom_arm_del[chrom] = [0, 0] + chrom_arm_loh[chrom] = [0, 0] chrom_arm_amp[chrom] = [0, 0] genome_size += p_size + q_size @@ -33,8 +36,8 @@ def create_tsv_report( log.info(f"Opening output tsv file: {output_txt}") sample_name = "" with open(output_txt, "w") as writer: - writer.write("sample\tgene(s)\tchrom\tregion\tcallers\tfreq_in_db\tcopy_number") - out_additional_only.write("sample\tgene(s)\tchrom\tregion\tcallers\tfreq_in_db\tcopy_number") + writer.write("sample\tgene(s)\tchrom\tregion\tcaller\tfreq_in_db\tcopy_number") + out_additional_only.write("sample\tgene(s)\tchrom\tregion\tcaller\tfreq_in_db\tcopy_number") file1 = True for input_org_vcf in input_org_vcfs: del_1p19q = { @@ -58,24 +61,24 @@ def create_tsv_report( start = variant.pos end = variant.pos + int(utils.get_annotation_data_info(variant, "SVLEN")) - 1 size = end - start + 1 - callers = utils.get_annotation_data_info(variant, "CALLER") + caller = utils.get_annotation_data_info(variant, "CALLER") cn = utils.get_annotation_data_info(variant, "CORR_CN") AF = utils.get_annotation_data_info(variant, "Twist_AF") BAF = utils.get_annotation_data_info(variant, "BAF") - if BAF != "": + if BAF: BAF = float(BAF) if AF is None: AF = 0.0 # 1p19q deletion if cn < del_1p19q_cn and chr == "chr1" and start >= del_1p19q["1p"][0] and start <= del_1p19q["1p"][1]: - if callers == "cnvkit": + if caller == "cnvkit": del_1p19q["1p_cnvkit"] += size - elif callers == "gatk": + elif caller == "gatk": del_1p19q["1p_gatkcnv"] += size if cn < del_1p19q_cn and chr == "chr19" and start >= del_1p19q["19q"][0] and start <= del_1p19q["19q"][1]: - if callers == "cnvkit": + if caller == "cnvkit": del_1p19q["19q_cnvkit"] += size - elif callers == "gatk": + elif caller == "gatk": del_1p19q["19q_gatkcnv"] += size # Large chromosome CNV if file1: @@ -84,6 +87,11 @@ def create_tsv_report( chrom_arm_del[chr][0] += size else: chrom_arm_del[chr][1] += size + if cn > normal_cn_lower_limit and cn < normal_cn_upper_limit and BAF and (BAF < normal_baf_lower_limit or BAF > normal_baf_upper_limit): + if start >= chrom_arm_size[chr][0][0] and start <= chrom_arm_size[chr][0][1]: + chrom_arm_loh[chr][0] += size + else: + chrom_arm_loh[chr][1] += size if cn > amp_chr_arm_cn_limit and caller == "cnvkit": if start >= chrom_arm_size[chr][0][0] and start <= chrom_arm_size[chr][0][1]: chrom_arm_amp[chr][0] += size @@ -91,7 +99,7 @@ def create_tsv_report( chrom_arm_amp[chr][1] += size # Baseline check if file1: - if cn > 1.8 and cn < 2.2: + if cn > normal_cn_lower_limit and cn < normal_cn_upper_limit: if caller == "cnvkit": baseline[0] += size else: @@ -99,26 +107,26 @@ def create_tsv_report( # Poliploidy check if file1: if caller == "cnvkit": - if cn > 1.8 and cn < 2.2 and BAF != "" and (BAF < 0.3 or BAF > 0.7): + if cn > normal_cn_lower_limit and cn < normal_cn_upper_limit and BAF and (BAF < normal_baf_lower_limit or BAF > normal_baf_upper_limit): polyploidy += size - elif cn > 2.5 and BAF != "" and (BAF > 0.4 and BAF < 0.6): + elif cn > amp_chr_arm_cn_limit and BAF and (BAF > normal_baf_lower_limit and BAF < normal_baf_upper_limit): polyploidy += size - elif cn < 1.4 and BAF != "" and (BAF > 0.4 and BAF < 0.6): + elif cn < del_chr_arm_cn_limit and BAF and (BAF > normal_baf_lower_limit and BAF < normal_baf_upper_limit): polyploidy += size if genes is not None: for gene in genes.split(","): if gene not in gene_all_dict: gene_all_dict[gene] = [] - gene_all_dict[gene].append([chr, start, end, callers, cn, AF]) + gene_all_dict[gene].append([chr, start, end, caller, cn, AF]) else: duplicate = False for variant in gene_all_dict[gene]: - if chr == variant[0] and start == variant[1] and end == variant[2] and callers == variant[3]: + if chr == variant[0] and start == variant[1] and end == variant[2] and caller == variant[3]: duplicate = True break if not duplicate: - gene_all_dict[gene].append([chr, start, end, callers, cn, AF]) + gene_all_dict[gene].append([chr, start, end, caller, cn, AF]) if (del_1p19q["1p_cnvkit"] / del_1p19q["1p"][2] > del_1p19q_chr_arm_fraction and del_1p19q["19q_cnvkit"] / del_1p19q["19q"][2] > del_1p19q_chr_arm_fraction): if nr_writes < 2: @@ -152,17 +160,17 @@ def create_tsv_report( chr = variant.chrom start = variant.pos end = variant.pos + int(utils.get_annotation_data_info(variant, "SVLEN")) - 1 - callers = utils.get_annotation_data_info(variant, "CALLER") + caller = utils.get_annotation_data_info(variant, "CALLER") cn = utils.get_annotation_data_info(variant, "CORR_CN") AF = utils.get_annotation_data_info(variant, "Twist_AF") if AF is None: AF = 0.0 - writer.write(f"\n{samples}\t{genes}\t{chr}\t{start}-{end}\t{callers}\t{AF:.2f}\t{cn:.2f}") + writer.write(f"\n{samples}\t{genes}\t{chr}\t{start}-{end}\t{caller}\t{AF:.2f}\t{cn:.2f}") counter += 1 for gene in genes.split(","): if gene not in gene_variant_dict: gene_variant_dict[gene] = [] - gene_variant_dict[gene].append([chr, start, end, callers, cn, AF]) + gene_variant_dict[gene].append([chr, start, end, caller, cn, AF]) for gene in gene_variant_dict: if len(gene_variant_dict[gene]) == 1: caller = gene_variant_dict[gene][0][3] @@ -171,7 +179,7 @@ def create_tsv_report( chr = cnv[0] start = cnv[1] end = cnv[2] - callers = cnv[3] + caller = cnv[3] cn = cnv[4] AF = cnv[5] if ( @@ -180,7 +188,7 @@ def create_tsv_report( (gene_variant_dict[gene][0][1] >= start and gene_variant_dict[gene][0][1] <= end) or (gene_variant_dict[gene][0][2] >= end and gene_variant_dict[gene][0][2] <= start) ): - writer.write(f"\n{samples}\t{gene}\t{chr}\t{start}-{end}\t{callers}\t{AF:.2f}\t{cn:.2f}") + writer.write(f"\n{samples}\t{gene}\t{chr}\t{start}-{end}\t{caller}\t{AF:.2f}\t{cn:.2f}") log.info(f"Processed {counter} variants") deletions = open(input_del) @@ -191,15 +199,15 @@ def create_tsv_report( chr = columns['Chromosome'] start = columns['Gene_start'] end = columns['Gene_end'] - callers = "small_deletion" + caller = "small_deletion" AF = "NA" log_odds_ratio = float(columns['Median_L2R_deletion']) cn = 2*pow(2, float(log_odds_ratio)) ccn = cn if TC > 0.0: ccn = round(2 + (cn - 2) * (1/float(TC)), 2) - writer.write(f"\n{sample_name}\t{gene}\t{chr}\t{start}-{end}\t{callers}\t{AF}\t{ccn:.2f}") - out_additional_only.write(f"\n{sample_name}\t{gene}\t{chr}\t{start}-{end}\t{callers}\t{AF}\t{ccn:.2f}") + writer.write(f"\n{sample_name}\t{gene}\t{chr}\t{start}-{end}\t{caller}\t{AF}\t{ccn:.2f}") + out_additional_only.write(f"\n{sample_name}\t{gene}\t{chr}\t{start}-{end}\t{caller}\t{AF}\t{ccn:.2f}") amplifications = open(input_amp) header_list = next(amplifications).split("\t") for amplification in amplifications: @@ -208,7 +216,7 @@ def create_tsv_report( chr = columns['Chromosome'] start = columns['Gene_start'] end = columns['Gene_end'] - callers = "small_amplification" + caller = "small_amplification" AF = "NA" log_odds_ratio = float(columns['Median_L2R_amplification']) cn = 2*pow(2, float(log_odds_ratio)) @@ -216,29 +224,30 @@ def create_tsv_report( if TC > 0.0: ccn = round(2 + (cn - 2) * (1/float(TC)), 2) if ccn > amp_cn_limit: - writer.write(f"\n{sample_name}\t{gene}\t{chr}\t{start}-{end}\t{callers}\t{AF}\t{ccn:.2f}") - out_additional_only.write(f"\n{sample_name}\t{gene}\t{chr}\t{start}-{end}\t{callers}\t{AF}\t{ccn:.2f}") + writer.write(f"\n{sample_name}\t{gene}\t{chr}\t{start}-{end}\t{caller}\t{AF}\t{ccn:.2f}") + out_additional_only.write(f"\n{sample_name}\t{gene}\t{chr}\t{start}-{end}\t{caller}\t{AF}\t{ccn:.2f}") with open(out_tsv_chrom_arms, "w") as writer: - print(baseline[0] / genome_size) - print(baseline[1] / genome_size) - print(polyploidy / genome_size) writer.write("chrom\tarm\tcaller\ttype\tfraction") if baseline[0] / genome_size < 0.2: - writer.write(f"\nWarning: baseline of GATK CNV might not ne correct!") + writer.write(f"\nWarning: baseline (log2ratio = 0) of GATK CNV might not be correct!") if baseline[1] / genome_size < 0.2: - writer.write(f"\nWarning: baseline of CNVkit might not ne correct!") + writer.write(f"\nWarning: baseline (log2ratio = 0) of CNVkit might not be correct!") if polyploidy / genome_size > 0.5: writer.write(f"\nWarning: potential polyploidy detected!") for chrom in chrom_arm_del: - if chrom_arm_del[chrom][0] / chrom_arm_size[chrom][0] > chr_arm_fraction: - writer.write(f"\n{chrom}\tp\tcnvkit\tdeletion\t{chrom_arm_del[chrom][0] * 100 / chrom_arm_size[chrom][0]}%") - if chrom_arm_del[chrom][1] / chrom_arm_size[chrom][1] > chr_arm_fraction: - writer.write(f"\n{chrom}\tp\tcnvkit\tdeletion\t{chrom_arm_del[chrom][1] * 100 / chrom_arm_size[chrom][1]}%") - if chrom_arm_amp[chrom][0] / chrom_arm_size[chrom][0] > chr_arm_fraction: - writer.write(f"\n{chrom}\tp\tcnvkit\tduplication\t{chrom_arm_amp[chrom][0] * 100 / chrom_arm_size[chrom][0]}%") - if chrom_arm_amp[chrom][1] / chrom_arm_size[chrom][1] > chr_arm_fraction: - writer.write(f"\n{chrom}\tp\tcnvkit\tduplication\t{chrom_arm_amp[chrom][1] * 100 / chrom_arm_size[chrom][1]}%") + if chrom_arm_del[chrom][0] / chrom_arm_size[chrom][0][2] > chr_arm_fraction: + writer.write(f"\n{chrom}\tp\tcnvkit\tdeletion\t{chrom_arm_del[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") + if chrom_arm_del[chrom][1] / chrom_arm_size[chrom][1][2] > chr_arm_fraction: + writer.write(f"\n{chrom}\tq\tcnvkit\tdeletion\t{chrom_arm_del[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") + if chrom_arm_loh[chrom][0] / chrom_arm_size[chrom][0][2] > chr_arm_fraction: + writer.write(f"\n{chrom}\tp\tcnvkit\tloh\t{chrom_arm_loh[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") + if chrom_arm_loh[chrom][1] / chrom_arm_size[chrom][1][2] > chr_arm_fraction: + writer.write(f"\n{chrom}\tq\tcnvkit\tloh\t{chrom_arm_loh[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") + if chrom_arm_amp[chrom][0] / chrom_arm_size[chrom][0][2] > chr_arm_fraction: + writer.write(f"\n{chrom}\tp\tcnvkit\tduplication\t{chrom_arm_amp[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") + if chrom_arm_amp[chrom][1] / chrom_arm_size[chrom][1][2] > chr_arm_fraction: + writer.write(f"\n{chrom}\tq\tcnvkit\tduplication\t{chrom_arm_amp[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") if __name__ == "__main__": @@ -255,6 +264,10 @@ def create_tsv_report( chr_arm_fraction = snakemake.params.chr_arm_fraction del_chr_arm_cn_limit = snakemake.params.del_chr_arm_cn_limit amp_chr_arm_cn_limit = snakemake.params.amp_chr_arm_cn_limit + normal_cn_lower_limit = snakemake.params.normal_cn_lower_limit + normal_cn_upper_limit = snakemake.params.normal_cn_upper_limit + normal_baf_lower_limit = snakemake.params.normal_cn_lower_limit + normal_baf_upper_limit = snakemake.params.normal_cn_upper_limit TC = float(snakemake.params.tc) with open(snakemake.output.tsv_additional_only, "w") as out_additional_only: create_tsv_report( @@ -272,5 +285,9 @@ def create_tsv_report( chr_arm_fraction, del_chr_arm_cn_limit, amp_chr_arm_cn_limit, + normal_cn_lower_limit, + normal_cn_upper_limit, + normal_baf_lower_limit, + normal_baf_upper_limit, TC, ) From 8a508ad13188648eeb08f4d38d5870cf246aa8f8 Mon Sep 17 00:00:00 2001 From: jonca79 Date: Wed, 17 Apr 2024 16:20:16 +0200 Subject: [PATCH 16/40] fix: handle CNVs bridging the chromosome arms --- workflow/rules/cnv_tsv_report.smk | 2 +- workflow/rules/common.smk | 2 +- workflow/scripts/cnv_report.py | 79 +++++++++++++++++++------------ 3 files changed, 52 insertions(+), 31 deletions(-) diff --git a/workflow/rules/cnv_tsv_report.smk b/workflow/rules/cnv_tsv_report.smk index b8039cb2..80ba536f 100644 --- a/workflow/rules/cnv_tsv_report.smk +++ b/workflow/rules/cnv_tsv_report.smk @@ -28,7 +28,7 @@ rule cnv_tsv_report: chr_arm_fraction=config.get("cnv_tsv_report", {}).get("chr_arm_fraction", ""), del_chr_arm_cn_limit=config.get("cnv_tsv_report", {}).get("del_chr_arm_cn_limit", ""), del_1p19q_cn_limit=config.get("cnv_tsv_report", {}).get("del_1p19q_cn_limit", ""), - del_1p19q_chr_arm_fraction=config.get("cnv_tsv_report", {}).get("del_1p19q_chr_arm_fraction", ""), + del_1p19q_chr_arm_fraction=config.get("cnv_tsv_report", {}).get("del_1p19q_chr_arm_fraction", ""), normal_cn_lower_limit=config.get("cnv_tsv_report", {}).get("normal_cn_lower_limit", ""), normal_cn_upper_limit=config.get("cnv_tsv_report", {}).get("normal_cn_upper_limit", ""), normal_baf_lower_limit=config.get("cnv_tsv_report", {}).get("normal_cn_lower_limit", ""), diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index 8348099a..9b72b638 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -74,7 +74,7 @@ with open(config["output"]) as output: validate(output_spec, schema="../schemas/output_files.schema.yaml") -date_string = datetime.now().strftime('%Y%m%d') +date_string = datetime.now().strftime("%Y%m%d") pipeline_version = get_pipeline_version(workflow, pipeline_name="Twist_Solid") version_files = touch_pipeline_verion_file_name(pipeline_version, date_string=date_string, directory="results/versions/software") if use_container(workflow): diff --git a/workflow/scripts/cnv_report.py b/workflow/scripts/cnv_report.py index 52cb9c4e..f37270e2 100644 --- a/workflow/scripts/cnv_report.py +++ b/workflow/scripts/cnv_report.py @@ -9,7 +9,7 @@ def create_tsv_report( input_vcfs, input_org_vcfs, input_del, input_amp, in_chrom_arm_size, amp_cn_limit, output_txt, out_additional_only, out_tsv_chrom_arms, del_1p19q_cn, del_1p19q_chr_arm_fraction, chr_arm_fraction, del_chr_arm_cn_limit, amp_chr_arm_cn_limit, normal_cn_lower_limit, normal_cn_upper_limit, - normal_baf_lower_limit, normal_baf_upper_limit,TC + normal_baf_lower_limit, normal_baf_upper_limit, TC ): chrom_arm_size = {} chrom_arm_del = {} @@ -65,6 +65,16 @@ def create_tsv_report( cn = utils.get_annotation_data_info(variant, "CORR_CN") AF = utils.get_annotation_data_info(variant, "Twist_AF") BAF = utils.get_annotation_data_info(variant, "BAF") + p_size = 0 + q_size = 0 + if start >= chrom_arm_size[chr][0][0] and start <= chrom_arm_size[chr][0][1]: + if end <= chrom_arm_size[chr][0][0] and end <= chrom_arm_size[chr][0][1] : + p_size = size + else: + p_size = chrom_arm_size[chr][0][1] - start + 1 + q_size = end - chrom_arm_size[chr][0][1] + else: + q_size = size if BAF: BAF = float(BAF) if AF is None: @@ -72,31 +82,29 @@ def create_tsv_report( # 1p19q deletion if cn < del_1p19q_cn and chr == "chr1" and start >= del_1p19q["1p"][0] and start <= del_1p19q["1p"][1]: if caller == "cnvkit": - del_1p19q["1p_cnvkit"] += size + del_1p19q["1p_cnvkit"] += p_size elif caller == "gatk": - del_1p19q["1p_gatkcnv"] += size + del_1p19q["1p_gatkcnv"] += p_size if cn < del_1p19q_cn and chr == "chr19" and start >= del_1p19q["19q"][0] and start <= del_1p19q["19q"][1]: if caller == "cnvkit": - del_1p19q["19q_cnvkit"] += size + del_1p19q["19q_cnvkit"] += q_size elif caller == "gatk": - del_1p19q["19q_gatkcnv"] += size + del_1p19q["19q_gatkcnv"] += q_size # Large chromosome CNV if file1: - if cn < del_chr_arm_cn_limit and caller == "cnvkit": - if start >= chrom_arm_size[chr][0][0] and start <= chrom_arm_size[chr][0][1]: - chrom_arm_del[chr][0] += size - else: - chrom_arm_del[chr][1] += size - if cn > normal_cn_lower_limit and cn < normal_cn_upper_limit and BAF and (BAF < normal_baf_lower_limit or BAF > normal_baf_upper_limit): - if start >= chrom_arm_size[chr][0][0] and start <= chrom_arm_size[chr][0][1]: - chrom_arm_loh[chr][0] += size - else: - chrom_arm_loh[chr][1] += size - if cn > amp_chr_arm_cn_limit and caller == "cnvkit": - if start >= chrom_arm_size[chr][0][0] and start <= chrom_arm_size[chr][0][1]: - chrom_arm_amp[chr][0] += size - else: - chrom_arm_amp[chr][1] += size + if caller == "cnvkit": + if cn < del_chr_arm_cn_limit: + chrom_arm_del[chr][0] += p_size + chrom_arm_del[chr][1] += q_size + if ( + cn > normal_cn_lower_limit and cn < normal_cn_upper_limit and + BAF and (BAF < normal_baf_lower_limit or BAF > normal_baf_upper_limit) + ): + chrom_arm_loh[chr][0] += p_size + chrom_arm_loh[chr][1] += q_size + if cn > amp_chr_arm_cn_limit: + chrom_arm_amp[chr][0] += p_size + chrom_arm_amp[chr][1] += q_size # Baseline check if file1: if cn > normal_cn_lower_limit and cn < normal_cn_upper_limit: @@ -107,11 +115,20 @@ def create_tsv_report( # Poliploidy check if file1: if caller == "cnvkit": - if cn > normal_cn_lower_limit and cn < normal_cn_upper_limit and BAF and (BAF < normal_baf_lower_limit or BAF > normal_baf_upper_limit): + if ( + cn > normal_cn_lower_limit and cn < normal_cn_upper_limit and + BAF and (BAF < normal_baf_lower_limit or BAF > normal_baf_upper_limit) + ): polyploidy += size - elif cn > amp_chr_arm_cn_limit and BAF and (BAF > normal_baf_lower_limit and BAF < normal_baf_upper_limit): + elif ( + cn > amp_chr_arm_cn_limit and + BAF and (BAF > normal_baf_lower_limit and BAF < normal_baf_upper_limit) + ): polyploidy += size - elif cn < del_chr_arm_cn_limit and BAF and (BAF > normal_baf_lower_limit and BAF < normal_baf_upper_limit): + elif ( + cn < del_chr_arm_cn_limit and + BAF and (BAF > normal_baf_lower_limit and BAF < normal_baf_upper_limit) + ): polyploidy += size if genes is not None: @@ -237,17 +254,21 @@ def create_tsv_report( writer.write(f"\nWarning: potential polyploidy detected!") for chrom in chrom_arm_del: if chrom_arm_del[chrom][0] / chrom_arm_size[chrom][0][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tp\tcnvkit\tdeletion\t{chrom_arm_del[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") + writer.write(f"\n{chrom}\tp\tcnvkit\tdeletion\t") + writer.write(f"{chrom_arm_del[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") if chrom_arm_del[chrom][1] / chrom_arm_size[chrom][1][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tq\tcnvkit\tdeletion\t{chrom_arm_del[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") + writer.write(f"\n{chrom}\tq\tcnvkit\tdeletion\t") + writer.write(f"{chrom_arm_del[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") if chrom_arm_loh[chrom][0] / chrom_arm_size[chrom][0][2] > chr_arm_fraction: writer.write(f"\n{chrom}\tp\tcnvkit\tloh\t{chrom_arm_loh[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") if chrom_arm_loh[chrom][1] / chrom_arm_size[chrom][1][2] > chr_arm_fraction: writer.write(f"\n{chrom}\tq\tcnvkit\tloh\t{chrom_arm_loh[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") if chrom_arm_amp[chrom][0] / chrom_arm_size[chrom][0][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tp\tcnvkit\tduplication\t{chrom_arm_amp[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") + writer.write(f"\n{chrom}\tp\tcnvkit\tduplication\t") + writer.write(f"{chrom_arm_amp[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") if chrom_arm_amp[chrom][1] / chrom_arm_size[chrom][1][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tq\tcnvkit\tduplication\t{chrom_arm_amp[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") + writer.write(f"\n{chrom}\tq\tcnvkit\tduplication\t") + writer.write(f"{chrom_arm_amp[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") if __name__ == "__main__": @@ -266,8 +287,8 @@ def create_tsv_report( amp_chr_arm_cn_limit = snakemake.params.amp_chr_arm_cn_limit normal_cn_lower_limit = snakemake.params.normal_cn_lower_limit normal_cn_upper_limit = snakemake.params.normal_cn_upper_limit - normal_baf_lower_limit = snakemake.params.normal_cn_lower_limit - normal_baf_upper_limit = snakemake.params.normal_cn_upper_limit + normal_baf_lower_limit = snakemake.params.normal_baf_lower_limit + normal_baf_upper_limit = snakemake.params.normal_baf_upper_limit TC = float(snakemake.params.tc) with open(snakemake.output.tsv_additional_only, "w") as out_additional_only: create_tsv_report( From d46017212ef9a7cc077e090bb11d3c56c9dfb4d3 Mon Sep 17 00:00:00 2001 From: jonca79 Date: Wed, 17 Apr 2024 16:56:14 +0200 Subject: [PATCH 17/40] fix: variable baf bugfix --- workflow/rules/cnv_tsv_report.smk | 4 ++-- workflow/scripts/cnv_report.py | 16 ++++++++-------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/workflow/rules/cnv_tsv_report.smk b/workflow/rules/cnv_tsv_report.smk index 80ba536f..a5ebe015 100644 --- a/workflow/rules/cnv_tsv_report.smk +++ b/workflow/rules/cnv_tsv_report.smk @@ -31,8 +31,8 @@ rule cnv_tsv_report: del_1p19q_chr_arm_fraction=config.get("cnv_tsv_report", {}).get("del_1p19q_chr_arm_fraction", ""), normal_cn_lower_limit=config.get("cnv_tsv_report", {}).get("normal_cn_lower_limit", ""), normal_cn_upper_limit=config.get("cnv_tsv_report", {}).get("normal_cn_upper_limit", ""), - normal_baf_lower_limit=config.get("cnv_tsv_report", {}).get("normal_cn_lower_limit", ""), - normal_baf_upper_limit=config.get("cnv_tsv_report", {}).get("normal_cn_upper_limit", ""), + normal_baf_lower_limit=config.get("cnv_tsv_report", {}).get("normal_baf_lower_limit", ""), + normal_baf_upper_limit=config.get("cnv_tsv_report", {}).get("normal_baf_upper_limit", ""), tc=get_tc, log: "cnv_sv/svdb_query/{sample}_{type}.{tc_method}.{tag}.cnv_report.tsv.log", diff --git a/workflow/scripts/cnv_report.py b/workflow/scripts/cnv_report.py index f37270e2..42f5cdcb 100644 --- a/workflow/scripts/cnv_report.py +++ b/workflow/scripts/cnv_report.py @@ -68,7 +68,7 @@ def create_tsv_report( p_size = 0 q_size = 0 if start >= chrom_arm_size[chr][0][0] and start <= chrom_arm_size[chr][0][1]: - if end <= chrom_arm_size[chr][0][0] and end <= chrom_arm_size[chr][0][1] : + if end >= chrom_arm_size[chr][0][0] and end <= chrom_arm_size[chr][0][1]: p_size = size else: p_size = chrom_arm_size[chr][0][1] - start + 1 @@ -256,19 +256,19 @@ def create_tsv_report( if chrom_arm_del[chrom][0] / chrom_arm_size[chrom][0][2] > chr_arm_fraction: writer.write(f"\n{chrom}\tp\tcnvkit\tdeletion\t") writer.write(f"{chrom_arm_del[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") - if chrom_arm_del[chrom][1] / chrom_arm_size[chrom][1][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tq\tcnvkit\tdeletion\t") - writer.write(f"{chrom_arm_del[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") - if chrom_arm_loh[chrom][0] / chrom_arm_size[chrom][0][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tp\tcnvkit\tloh\t{chrom_arm_loh[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") - if chrom_arm_loh[chrom][1] / chrom_arm_size[chrom][1][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tq\tcnvkit\tloh\t{chrom_arm_loh[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") if chrom_arm_amp[chrom][0] / chrom_arm_size[chrom][0][2] > chr_arm_fraction: writer.write(f"\n{chrom}\tp\tcnvkit\tduplication\t") writer.write(f"{chrom_arm_amp[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") + if chrom_arm_loh[chrom][0] / chrom_arm_size[chrom][0][2] > chr_arm_fraction: + writer.write(f"\n{chrom}\tp\tcnvkit\tloh\t{chrom_arm_loh[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") + if chrom_arm_del[chrom][1] / chrom_arm_size[chrom][1][2] > chr_arm_fraction: + writer.write(f"\n{chrom}\tq\tcnvkit\tdeletion\t") + writer.write(f"{chrom_arm_del[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") if chrom_arm_amp[chrom][1] / chrom_arm_size[chrom][1][2] > chr_arm_fraction: writer.write(f"\n{chrom}\tq\tcnvkit\tduplication\t") writer.write(f"{chrom_arm_amp[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") + if chrom_arm_loh[chrom][1] / chrom_arm_size[chrom][1][2] > chr_arm_fraction: + writer.write(f"\n{chrom}\tq\tcnvkit\tloh\t{chrom_arm_loh[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") if __name__ == "__main__": From b1ce41711b33a9e076b7e23c73698d36f3244bb0 Mon Sep 17 00:00:00 2001 From: jonca79 Date: Wed, 17 Apr 2024 17:33:53 +0200 Subject: [PATCH 18/40] feat: decreased chr arm fraction --- config/config.yaml | 2 +- workflow/scripts/cnv_report.py | 16 ++++++++-------- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/config/config.yaml b/config/config.yaml index f5ac72da..870c39a7 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -86,7 +86,7 @@ cnv_tsv_report: chrom_arm_size: "{{PROJECT_DESIGN_DATA}}/GMS560/design/chromosome_arm_size.tsv" del_1p19q_cn_limit: 1.4 del_1p19q_chr_arm_fraction: 0.3 - chr_arm_fraction: 0.5 + chr_arm_fraction: 0.3 del_chr_arm_cn_limit: 1.4 amp_chr_arm_cn_limit: 2.5 normal_baf_lower_limit: 0.4 diff --git a/workflow/scripts/cnv_report.py b/workflow/scripts/cnv_report.py index 42f5cdcb..d00ffcd3 100644 --- a/workflow/scripts/cnv_report.py +++ b/workflow/scripts/cnv_report.py @@ -92,7 +92,7 @@ def create_tsv_report( del_1p19q["19q_gatkcnv"] += q_size # Large chromosome CNV if file1: - if caller == "cnvkit": + if caller == "gatk": if cn < del_chr_arm_cn_limit: chrom_arm_del[chr][0] += p_size chrom_arm_del[chr][1] += q_size @@ -114,7 +114,7 @@ def create_tsv_report( baseline[1] += size # Poliploidy check if file1: - if caller == "cnvkit": + if caller == "gatk": if ( cn > normal_cn_lower_limit and cn < normal_cn_upper_limit and BAF and (BAF < normal_baf_lower_limit or BAF > normal_baf_upper_limit) @@ -254,21 +254,21 @@ def create_tsv_report( writer.write(f"\nWarning: potential polyploidy detected!") for chrom in chrom_arm_del: if chrom_arm_del[chrom][0] / chrom_arm_size[chrom][0][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tp\tcnvkit\tdeletion\t") + writer.write(f"\n{chrom}\tp\tgatk_cnv\tdeletion\t") writer.write(f"{chrom_arm_del[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") if chrom_arm_amp[chrom][0] / chrom_arm_size[chrom][0][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tp\tcnvkit\tduplication\t") + writer.write(f"\n{chrom}\tp\tgatk_cnv\tduplication\t") writer.write(f"{chrom_arm_amp[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") if chrom_arm_loh[chrom][0] / chrom_arm_size[chrom][0][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tp\tcnvkit\tloh\t{chrom_arm_loh[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") + writer.write(f"\n{chrom}\tp\tgatk_cnv\tloh\t{chrom_arm_loh[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") if chrom_arm_del[chrom][1] / chrom_arm_size[chrom][1][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tq\tcnvkit\tdeletion\t") + writer.write(f"\n{chrom}\tq\tgatk_cnv\tdeletion\t") writer.write(f"{chrom_arm_del[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") if chrom_arm_amp[chrom][1] / chrom_arm_size[chrom][1][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tq\tcnvkit\tduplication\t") + writer.write(f"\n{chrom}\tq\tgatk_cnv\tduplication\t") writer.write(f"{chrom_arm_amp[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") if chrom_arm_loh[chrom][1] / chrom_arm_size[chrom][1][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tq\tcnvkit\tloh\t{chrom_arm_loh[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") + writer.write(f"\n{chrom}\tq\tgatk_cnv\tloh\t{chrom_arm_loh[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") if __name__ == "__main__": From e577cdd192036e240570d33cbc2a0d9cac8f59d3 Mon Sep 17 00:00:00 2001 From: jonca79 Date: Thu, 18 Apr 2024 09:39:38 +0200 Subject: [PATCH 19/40] feat: added table to cnv_html_report --- config/config.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/config/config.yaml b/config/config.yaml index 870c39a7..34371718 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -80,6 +80,12 @@ cnv_html_report: Additional small amplifications and deletions as well as 1p19q co-deletions called by Twist Solid in-house scripts. Can have overlaps with called regions from other callers. path: "cnv_sv/svdb_query/{sample}_{type}.{tc_method}.cnv_loh_genes_all.cnv_additional_variants_only.tsv" + - name: Large chromosomal aberrations. + description: > + Large chromosomal aberrations in the form of deletions, duplications and copy neutral loss of heterozygosity. + Also warnings of baseline skewness and detection of polyploidy in the sample. + path: "cnv_sv/svdb_query/{sample}_{type}.{tc_method}.cnv_loh_genes_all.cnv_chromosome_arms.tsv" + cnv_tsv_report: amp_cn_limit: 6.0 From 62c832d0979382d82233eb59421ab5ee6dbf7e14 Mon Sep 17 00:00:00 2001 From: jonca79 Date: Thu, 18 Apr 2024 09:46:07 +0200 Subject: [PATCH 20/40] docs: added config schemas for new params --- workflow/schemas/config.schema.yaml | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/workflow/schemas/config.schema.yaml b/workflow/schemas/config.schema.yaml index 33bfdb37..75d90172 100644 --- a/workflow/schemas/config.schema.yaml +++ b/workflow/schemas/config.schema.yaml @@ -119,6 +119,18 @@ properties: del_chr_arm_cn_limit: type: number description: Upper limit of copy number to be included in calculation of chr_arm_fraction for deletions + normal_cn_lower_limit: + type: number + description: Lower limit of copy number to be counted as a normal segment + normal_cn_upper_limit: + type: number + description: Upper limit of copy number to be counted as a normal segment + normal_baf_lower_limit: + type: number + description: Lower limit of BAF in segment to be counted as a normal segment + normal_baf_upper_limit: + type: number + description: Upper limit of BAF in segment to be counted as a normal segment cnvkit_batch: From 2d4eb4c4c7d35c6722ed3068a9acf2cd0f79a88e Mon Sep 17 00:00:00 2001 From: jonca79 Date: Thu, 18 Apr 2024 10:45:37 +0200 Subject: [PATCH 21/40] test: added params to test config --- .tests/integration/config/config.yaml | 4 ++++ config/config.yaml | 2 +- workflow/scripts/cnv_report.py | 34 +++++++++++++-------------- 3 files changed, 22 insertions(+), 18 deletions(-) diff --git a/.tests/integration/config/config.yaml b/.tests/integration/config/config.yaml index d6ad2859..8a1b1383 100644 --- a/.tests/integration/config/config.yaml +++ b/.tests/integration/config/config.yaml @@ -59,6 +59,10 @@ cnv_tsv_report: chr_arm_fraction: 0.5 del_chr_arm_cn_limit: 1.4 amp_chr_arm_cn_limit: 2.5 + normal_baf_lower_limit: 0.4 + normal_baf_upper_limit: 0.6 + normal_cn_lower_limit: 1.7 + normal_cn_upper_limit: 2.25 exon_skipping: design_bed: "reference/Twist_RNA_Design5.annotated.bed" diff --git a/config/config.yaml b/config/config.yaml index 34371718..95fdfc7a 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -80,7 +80,7 @@ cnv_html_report: Additional small amplifications and deletions as well as 1p19q co-deletions called by Twist Solid in-house scripts. Can have overlaps with called regions from other callers. path: "cnv_sv/svdb_query/{sample}_{type}.{tc_method}.cnv_loh_genes_all.cnv_additional_variants_only.tsv" - - name: Large chromosomal aberrations. + - name: Large chromosomal aberrations description: > Large chromosomal aberrations in the form of deletions, duplications and copy neutral loss of heterozygosity. Also warnings of baseline skewness and detection of polyploidy in the sample. diff --git a/workflow/scripts/cnv_report.py b/workflow/scripts/cnv_report.py index d00ffcd3..b87adf63 100644 --- a/workflow/scripts/cnv_report.py +++ b/workflow/scripts/cnv_report.py @@ -37,7 +37,7 @@ def create_tsv_report( sample_name = "" with open(output_txt, "w") as writer: writer.write("sample\tgene(s)\tchrom\tregion\tcaller\tfreq_in_db\tcopy_number") - out_additional_only.write("sample\tgene(s)\tchrom\tregion\tcaller\tfreq_in_db\tcopy_number") + out_additional_only.write("gene(s)\tchrom\tregion\tcaller\tfreq_in_db\tcopy_number") file1 = True for input_org_vcf in input_org_vcfs: del_1p19q = { @@ -92,7 +92,7 @@ def create_tsv_report( del_1p19q["19q_gatkcnv"] += q_size # Large chromosome CNV if file1: - if caller == "gatk": + if caller == "cnvkit": if cn < del_chr_arm_cn_limit: chrom_arm_del[chr][0] += p_size chrom_arm_del[chr][1] += q_size @@ -114,7 +114,7 @@ def create_tsv_report( baseline[1] += size # Poliploidy check if file1: - if caller == "gatk": + if caller == "cnvkit": if ( cn > normal_cn_lower_limit and cn < normal_cn_upper_limit and BAF and (BAF < normal_baf_lower_limit or BAF > normal_baf_upper_limit) @@ -148,13 +148,13 @@ def create_tsv_report( del_1p19q["19q_cnvkit"] / del_1p19q["19q"][2] > del_1p19q_chr_arm_fraction): if nr_writes < 2: writer.write(f"\n{samples}\t1p19q\tNA\tNA\tcnvkit\tNA\tNA") - out_additional_only.write(f"\n{samples}\t1p19q\tNA\tNA\tcnvkit\tNA\tNA") + out_additional_only.write(f"\n1p19q\tNA\tNA\tcnvkit\tNA\tNA") nr_writes += 1 if (del_1p19q["1p_gatkcnv"] / del_1p19q["1p"][2] > del_1p19q_chr_arm_fraction and del_1p19q["19q_gatkcnv"] / del_1p19q["19q"][2] > del_1p19q_chr_arm_fraction): if nr_writes < 2: writer.write(f"\n{samples}\t1p19q\tNA\tNA\tgatk_cnv\tNA\tNA") - out_additional_only.write(f"\n{samples}\t1p19q\tNA\tNA\tgatk_cnv\tNA\tNA") + out_additional_only.write(f"\nt1p19q\tNA\tNA\tgatk_cnv\tNA\tNA") nr_writes += 1 file1 = False @@ -224,7 +224,7 @@ def create_tsv_report( if TC > 0.0: ccn = round(2 + (cn - 2) * (1/float(TC)), 2) writer.write(f"\n{sample_name}\t{gene}\t{chr}\t{start}-{end}\t{caller}\t{AF}\t{ccn:.2f}") - out_additional_only.write(f"\n{sample_name}\t{gene}\t{chr}\t{start}-{end}\t{caller}\t{AF}\t{ccn:.2f}") + out_additional_only.write(f"\n{gene}\t{chr}\t{start}-{end}\t{caller}\t{AF}\t{ccn:.2f}") amplifications = open(input_amp) header_list = next(amplifications).split("\t") for amplification in amplifications: @@ -242,33 +242,33 @@ def create_tsv_report( ccn = round(2 + (cn - 2) * (1/float(TC)), 2) if ccn > amp_cn_limit: writer.write(f"\n{sample_name}\t{gene}\t{chr}\t{start}-{end}\t{caller}\t{AF}\t{ccn:.2f}") - out_additional_only.write(f"\n{sample_name}\t{gene}\t{chr}\t{start}-{end}\t{caller}\t{AF}\t{ccn:.2f}") + out_additional_only.write(f"\n{gene}\t{chr}\t{start}-{end}\t{caller}\t{AF}\t{ccn:.2f}") with open(out_tsv_chrom_arms, "w") as writer: writer.write("chrom\tarm\tcaller\ttype\tfraction") if baseline[0] / genome_size < 0.2: - writer.write(f"\nWarning: baseline (log2ratio = 0) of GATK CNV might not be correct!") + writer.write(f"\nWarning: baseline of GATK CNV might be shifted!\t\t\t\t{baseline[0] * 100 / genome_size:.1f}% on baseline") if baseline[1] / genome_size < 0.2: - writer.write(f"\nWarning: baseline (log2ratio = 0) of CNVkit might not be correct!") - if polyploidy / genome_size > 0.5: - writer.write(f"\nWarning: potential polyploidy detected!") + writer.write(f"\nWarning: baseline of CNVkit might be shifted!\t\t\t\t{baseline[1] * 100 / genome_size:.1f}% on baseline") + if polyploidy / genome_size > 0.2: + writer.write(f"\nWarning: potential polyploidy detected!\t\t\t\t{polyploidy * 100 / genome_size:.1f}% polyploid regions") for chrom in chrom_arm_del: if chrom_arm_del[chrom][0] / chrom_arm_size[chrom][0][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tp\tgatk_cnv\tdeletion\t") + writer.write(f"\n{chrom}\tp\tcnvkit\tdeletion\t") writer.write(f"{chrom_arm_del[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") if chrom_arm_amp[chrom][0] / chrom_arm_size[chrom][0][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tp\tgatk_cnv\tduplication\t") + writer.write(f"\n{chrom}\tp\tcnvkit\tduplication\t") writer.write(f"{chrom_arm_amp[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") if chrom_arm_loh[chrom][0] / chrom_arm_size[chrom][0][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tp\tgatk_cnv\tloh\t{chrom_arm_loh[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") + writer.write(f"\n{chrom}\tp\tcnvkit\tloh\t{chrom_arm_loh[chrom][0] * 100 / chrom_arm_size[chrom][0][2]:.1f}%") if chrom_arm_del[chrom][1] / chrom_arm_size[chrom][1][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tq\tgatk_cnv\tdeletion\t") + writer.write(f"\n{chrom}\tq\tcnvkit\tdeletion\t") writer.write(f"{chrom_arm_del[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") if chrom_arm_amp[chrom][1] / chrom_arm_size[chrom][1][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tq\tgatk_cnv\tduplication\t") + writer.write(f"\n{chrom}\tq\tcnvkit\tduplication\t") writer.write(f"{chrom_arm_amp[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") if chrom_arm_loh[chrom][1] / chrom_arm_size[chrom][1][2] > chr_arm_fraction: - writer.write(f"\n{chrom}\tq\tgatk_cnv\tloh\t{chrom_arm_loh[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") + writer.write(f"\n{chrom}\tq\tcnvkit\tloh\t{chrom_arm_loh[chrom][1] * 100 / chrom_arm_size[chrom][1][2]:.1f}%") if __name__ == "__main__": From 8f91b42a5509fec983c1c077d53c499c035e955a Mon Sep 17 00:00:00 2001 From: jonca79 Date: Thu, 18 Apr 2024 14:25:24 +0200 Subject: [PATCH 22/40] feat: added configuration of polyploidy and baseline limits --- config/config.yaml | 2 ++ workflow/rules/cnv_tsv_report.smk | 2 ++ workflow/schemas/config.schema.yaml | 6 ++++++ workflow/scripts/cnv_report.py | 21 ++++++++++++++------- 4 files changed, 24 insertions(+), 7 deletions(-) diff --git a/config/config.yaml b/config/config.yaml index 95fdfc7a..9cb28caa 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -89,6 +89,7 @@ cnv_html_report: cnv_tsv_report: amp_cn_limit: 6.0 + baseline_fraction_limit: 0.2 chrom_arm_size: "{{PROJECT_DESIGN_DATA}}/GMS560/design/chromosome_arm_size.tsv" del_1p19q_cn_limit: 1.4 del_1p19q_chr_arm_fraction: 0.3 @@ -99,6 +100,7 @@ cnv_tsv_report: normal_baf_upper_limit: 0.6 normal_cn_lower_limit: 1.7 normal_cn_upper_limit: 2.25 + polyploidy_fraction_limit: 0.2 fastp_pe: container: "docker://hydragenetics/fastp:0.20.1" diff --git a/workflow/rules/cnv_tsv_report.smk b/workflow/rules/cnv_tsv_report.smk index a5ebe015..d7fcbb04 100644 --- a/workflow/rules/cnv_tsv_report.smk +++ b/workflow/rules/cnv_tsv_report.smk @@ -24,6 +24,7 @@ rule cnv_tsv_report: tsv_chrom_arms=temp("cnv_sv/svdb_query/{sample}_{type}.{tc_method}.{tag}.cnv_chromosome_arms.tsv"), params: amp_chr_arm_cn_limit=config.get("cnv_tsv_report", {}).get("amp_chr_arm_cn_limit", ""), + baseline_fraction_limit=config.get("cnv_tsv_report", {}).get("baseline_fraction_limit", ""), call_small_amplifications_cn_limit=config.get("cnv_tsv_report", {}).get("amp_cn_limit", ""), chr_arm_fraction=config.get("cnv_tsv_report", {}).get("chr_arm_fraction", ""), del_chr_arm_cn_limit=config.get("cnv_tsv_report", {}).get("del_chr_arm_cn_limit", ""), @@ -33,6 +34,7 @@ rule cnv_tsv_report: normal_cn_upper_limit=config.get("cnv_tsv_report", {}).get("normal_cn_upper_limit", ""), normal_baf_lower_limit=config.get("cnv_tsv_report", {}).get("normal_baf_lower_limit", ""), normal_baf_upper_limit=config.get("cnv_tsv_report", {}).get("normal_baf_upper_limit", ""), + polyploidy_fraction_limit=config.get("cnv_tsv_report", {}).get("polyploidy_fraction_limit", ""), tc=get_tc, log: "cnv_sv/svdb_query/{sample}_{type}.{tc_method}.{tag}.cnv_report.tsv.log", diff --git a/workflow/schemas/config.schema.yaml b/workflow/schemas/config.schema.yaml index 75d90172..298b94f2 100644 --- a/workflow/schemas/config.schema.yaml +++ b/workflow/schemas/config.schema.yaml @@ -101,6 +101,9 @@ properties: amp_chr_arm_cn_limit: type: number description: Lower limit of copy number to be included in calculation of chr_arm_fraction for duplications + baseline_fraction_limit: + type: number + description: Lower limit of fraction with neutral copy segments and neutral BAF values. A warning of potentially incorrect baseline is reported otherwise. container: type: string description: name or path to docker/singularity container @@ -131,6 +134,9 @@ properties: normal_baf_upper_limit: type: number description: Upper limit of BAF in segment to be counted as a normal segment + polyploidy_fraction_limit: + type: number + description: Upper limit of fraction with aberrant BAF / copy number segment combination. A warning of potential polyploidy is reported otherwise. cnvkit_batch: diff --git a/workflow/scripts/cnv_report.py b/workflow/scripts/cnv_report.py index b87adf63..54784d2d 100644 --- a/workflow/scripts/cnv_report.py +++ b/workflow/scripts/cnv_report.py @@ -9,7 +9,7 @@ def create_tsv_report( input_vcfs, input_org_vcfs, input_del, input_amp, in_chrom_arm_size, amp_cn_limit, output_txt, out_additional_only, out_tsv_chrom_arms, del_1p19q_cn, del_1p19q_chr_arm_fraction, chr_arm_fraction, del_chr_arm_cn_limit, amp_chr_arm_cn_limit, normal_cn_lower_limit, normal_cn_upper_limit, - normal_baf_lower_limit, normal_baf_upper_limit, TC + normal_baf_lower_limit, normal_baf_upper_limit, baseline_fraction_limit, polyploidy_fraction_limit, TC ): chrom_arm_size = {} chrom_arm_del = {} @@ -246,12 +246,15 @@ def create_tsv_report( with open(out_tsv_chrom_arms, "w") as writer: writer.write("chrom\tarm\tcaller\ttype\tfraction") - if baseline[0] / genome_size < 0.2: - writer.write(f"\nWarning: baseline of GATK CNV might be shifted!\t\t\t\t{baseline[0] * 100 / genome_size:.1f}% on baseline") - if baseline[1] / genome_size < 0.2: - writer.write(f"\nWarning: baseline of CNVkit might be shifted!\t\t\t\t{baseline[1] * 100 / genome_size:.1f}% on baseline") - if polyploidy / genome_size > 0.2: - writer.write(f"\nWarning: potential polyploidy detected!\t\t\t\t{polyploidy * 100 / genome_size:.1f}% polyploid regions") + if baseline[0] / genome_size < baseline_fraction_limit: + writer.write(f"\nWarning: baseline of GATK CNV might be shifted!\t\t\t\t") + writer.write(f"{baseline[0] * 100 / genome_size:.1f}% on baseline") + if baseline[1] / genome_size < baseline_fraction_limit: + writer.write(f"\nWarning: baseline of CNVkit might be shifted!\t\t\t\t") + writer.write(f"{baseline[1] * 100 / genome_size:.1f}% on baseline") + if polyploidy / genome_size > polyploidy_fraction_limit: + writer.write(f"\nWarning: potential polyploidy detected!\t\t\t\t") + writer.write(f"{polyploidy * 100 / genome_size:.1f}% polyploid regions") for chrom in chrom_arm_del: if chrom_arm_del[chrom][0] / chrom_arm_size[chrom][0][2] > chr_arm_fraction: writer.write(f"\n{chrom}\tp\tcnvkit\tdeletion\t") @@ -289,6 +292,8 @@ def create_tsv_report( normal_cn_upper_limit = snakemake.params.normal_cn_upper_limit normal_baf_lower_limit = snakemake.params.normal_baf_lower_limit normal_baf_upper_limit = snakemake.params.normal_baf_upper_limit + baseline_fraction_limit = snakemake.params.baseline_fraction_limit + polyploidy_fraction_limit = snakemake.params.polyploidy_fraction_limit TC = float(snakemake.params.tc) with open(snakemake.output.tsv_additional_only, "w") as out_additional_only: create_tsv_report( @@ -310,5 +315,7 @@ def create_tsv_report( normal_cn_upper_limit, normal_baf_lower_limit, normal_baf_upper_limit, + baseline_fraction_limit, + polyploidy_fraction_limit, TC, ) From 4f62f573e26ffc25b1e490727d978f07eaa0929d Mon Sep 17 00:00:00 2001 From: jonca79 Date: Thu, 18 Apr 2024 15:21:30 +0200 Subject: [PATCH 23/40] test: added unit tests --- .tests/units/test_cnv_report.py | 64 ++++++++++++++++++++++++++++++++- .tests/units/vcf/test.cnv2.vcf | 1 + 2 files changed, 64 insertions(+), 1 deletion(-) diff --git a/.tests/units/test_cnv_report.py b/.tests/units/test_cnv_report.py index 212436f2..1b10d17c 100644 --- a/.tests/units/test_cnv_report.py +++ b/.tests/units/test_cnv_report.py @@ -15,16 +15,28 @@ class TestGetCaller(unittest.TestCase): def test_create_tsv_report(self): cnv = tempfile.mkdtemp() + "/tcnv.txt" out_additional_only = open(tempfile.mkdtemp() + "/out_additional_only.txt", "w") + out_tsv_chrom_arms = tempfile.mkdtemp() + "/cnv_chromosome_arms.tsv" create_tsv_report( [".tests/units/vcf/test.cnv1.vcf"], [".tests/units/vcf/test.cnv2.vcf"], ".tests/units/vcf/test.deletions.tsv", ".tests/units/vcf/test.amplifications.tsv", + ".tests/integration/reference/chromosome_arm_size.tsv", 2.0, cnv, out_additional_only, + out_tsv_chrom_arms, 1.5, 0.5, + 0.3, + 1.4, + 2.5, + 1.7, + 2.25, + 0.4, + 0.6, + 0.2, + 0.2, 0.5, ) @@ -36,7 +48,7 @@ class TestCase: testcases = [ TestCase( name="header row", - expected=("sample", "gene(s)", "chrom", "region", "callers", "freq_in_db", "copy_number") + expected=("sample", "gene(s)", "chrom", "region", "caller", "freq_in_db", "copy_number") ), TestCase( name="variant 1", @@ -60,6 +72,33 @@ class TestCase: ), ] + testcases2 = [ + TestCase( + name="header row", + expected=('chrom', 'arm', 'caller', 'type', 'fraction') + ), + TestCase( + name="baseline 1", + expected=("Warning: baseline of GATK CNV might be shifted!", '', '', '', "4.5% on baseline") + ), + TestCase( + name="baseline 2", + expected=("Warning: baseline of CNVkit might be shifted!", '', '', '', "0.0% on baseline") + ), + TestCase( + name="duplication", + expected=('chr8', 'q', 'cnvkit', 'duplication', '98.7%') + ), + TestCase( + name="loh 1", + expected=('chr9', 'p', 'cnvkit', 'loh', '97.5%') + ), + TestCase( + name="loh 2", + expected=('chr9', 'q', 'cnvkit', 'loh', '99.2%') + ), + ] + test_it = iter(testcases) with open(cnv) as reader: for line in reader: @@ -82,3 +121,26 @@ class TestCase: except StopIteration: print("More results than test cases") assert False + + test_it = iter(testcases2) + with open(out_tsv_chrom_arms) as reader: + for line in reader: + + actual = tuple(line.rstrip().split("\t")) + try: + case = next(test_it) + self.assertEqual( + case.expected, + actual, + "failed test '{}': expected {}, got {}".format( + case.name, case.expected, actual + ), + ) + except ValueError: + if case.expected == "ValueError": + assert True + else: + assert False + except StopIteration: + print("More results than test cases") + assert False diff --git a/.tests/units/vcf/test.cnv2.vcf b/.tests/units/vcf/test.cnv2.vcf index 85323925..dbdc8074 100644 --- a/.tests/units/vcf/test.cnv2.vcf +++ b/.tests/units/vcf/test.cnv2.vcf @@ -64,3 +64,4 @@ chr8 34370199 . N . . Genes=FGFR1;SVTYPE=DUP;END=43930232;SVLEN=9560034;LOG_ODDS_RATIO=2.10299;CALLER=cnvkit;CN=.;CORR_CN=8.59;PROBES=167;BAF=-1.1761;set=Intersection;SVDB_CHROM=.|chr8;SVDB_POS=.|34370199;SVDB_QUAL=.|.;SVDB_FILTERS=.|.;SVDB_SAMPLES=.|testSample_T|GT:0/1|CN:8.59|CNQ:167|DP:857.922|BAF:-1.1761;SVDB_INFO=.|SVTYPE:DUP|END:43930232|SVLEN:9560034|LOG_ODDS_RATIO:2.10299|CALLER:cnvkit|CN:NA|CORR_CN:8.59|PROBES:167|BAF:-1.1761;svdb_origin=testSample_T;Twist_OCC=3;Twist_AF=0.0103093 GT:CN:CNQ:DP:BAF 0/1:8.59:167:857.922:-1.1761 chr8 35008818 . N . . Genes=FGFR1,MYC;SVTYPE=DUP;END=146144253;SVLEN=111135436;LOG_ODDS_RATIO=0.58604;CALLER=gatk_cnv;CN=3;CORR_CN=7.01;PROBES=233;BAF=0.366555;BAF_PROBES=41;set=Intersection;SVDB_CHROM=.|chr8;SVDB_POS=.|35008818;SVDB_QUAL=.|.;SVDB_FILTERS=.|.;SVDB_SAMPLES=.|testSample_T|GT:0/1|CN:3.0|CCN:7.01|CNQ:233|BAF:0.366555|BAFQ:41;SVDB_INFO=.|SVTYPE:DUP|END:146144253|SVLEN:111135436|LOG_ODDS_RATIO:0.586040|CALLER:gatk_cnv|CN:3.0|CORR_CN:7.01|PROBES:233|BAF:0.366555|BAF_PROBES:41;svdb_origin=testSample_T;Twist_OCC=4;Twist_AF=0.0137457 GT:CN:CCN:CNQ:BAF:BAFQ 0/1:3:7.01:233:0.366555:41 chr8 46689525 . N . . Genes=MYC;SVTYPE=DUP;END=146144003;SVLEN=99454479;LOG_ODDS_RATIO=1.82064;CALLER=cnvkit;CN=.;CORR_CN=5.06;PROBES=991;BAF=-0.252241;set=Intersection;SVDB_CHROM=.|chr8;SVDB_POS=.|46689525;SVDB_QUAL=.|.;SVDB_FILTERS=.|.;SVDB_SAMPLES=.|testSample_T|GT:0/1|CN:7.06|CNQ:991|DP:287.108|BAF:-0.252241;SVDB_INFO=.|SVTYPE:DUP|END:146144003|SVLEN:99454479|LOG_ODDS_RATIO:1.82064|CALLER:cnvkit|CN:NA|CORR_CN:7.06|PROBES:991|BAF:-0.252241;svdb_origin=testSample_T;Twist_OCC=25;Twist_AF=0.0859107 GT:CN:CNQ:DP:BAF 0/1:7.06:991:287.108:-0.252241 +chr9 1206037 . N . . Genes=CDKN2A,CDKN2B,TSC1;SVTYPE=COPY_NORMAL;END=140509860;SVLEN=139303824;LOG_ODDS_RATIO=0.015690;CALLER=cnvkit;CN=2.02;CORR_CN=2.09;PROBES=640;BAF=0.386991;BAF_PROBES=79;set=Intersection;SVDB_CHROM=.|chr9;SVDB_POS=.|1206037;SVDB_QUAL=.|.;SVDB_FILTERS=.|.;SVDB_SAMPLES=.|testSample_T|GT:0/0|CN:2.02|CCN:2.09|CNQ:640|BAF:0.386991|BAFQ:79;SVDB_INFO=.|SVTYPE:COPY_NORMAL|END:140509860|SVLEN:139303824|LOG_ODDS_RATIO:0.015690|CALLER:gatk|CN:2.02|CORR_CN:2.09|PROBES:640|BAF:0.386991|BAF_PROBES:79;svdb_origin=testSample_T GT:CN:CCN:CNQ:BAF:BAFQ 0/0:2.02:2.09:640:0.386991:79 From c8264b2f887da62bc7231b580702b935a49a4a91 Mon Sep 17 00:00:00 2001 From: jonca79 <54137490+jonca79@users.noreply.github.com> Date: Fri, 19 Apr 2024 08:49:07 +0200 Subject: [PATCH 24/40] feat: two new amplification genes reported --- config/config.data.hg19.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/config/config.data.hg19.yaml b/config/config.data.hg19.yaml index 05dd0896..e4b2e68a 100644 --- a/config/config.data.hg19.yaml +++ b/config/config.data.hg19.yaml @@ -30,7 +30,7 @@ arriba_draw_fusion: protein_domains: "{{PROJECT_REF_DATA}}/ref_data/arriba_v2.3.0/protein_domains_hg19_hs37d5_GRCh37_v2.3.0.gff3" annotate_cnv: - cnv_amp_genes: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes.bed" + cnv_amp_genes: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes_240307.bed" cnv_loh_genes_validated: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_loh_uppsala_genes.bed" cnv_loh_genes_all: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_loh_genes.bed" @@ -57,7 +57,7 @@ call_small_cnv_deletions: regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_deletion_genes.tsv" call_small_cnv_amplifications: - regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amplification_genes.tsv" + regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amplification_genes_240307.tsv" cnvkit_batch: normal_reference: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_nextseq_36.cnn" From c6f7b5e2ef6aafd0d7dafcd50e1d6330cc8affc8 Mon Sep 17 00:00:00 2001 From: jonca79 <54137490+jonca79@users.noreply.github.com> Date: Fri, 19 Apr 2024 08:51:04 +0200 Subject: [PATCH 25/40] feat: new amp genes for hg38 --- config/config.data.hg38.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/config/config.data.hg38.yaml b/config/config.data.hg38.yaml index e7ed2052..15cb0881 100644 --- a/config/config.data.hg38.yaml +++ b/config/config.data.hg38.yaml @@ -30,7 +30,7 @@ arriba_draw_fusion: protein_domains: "{{PROJECT_REF_DATA}}/ref_data/arriba_v2.3.0/protein_domains_hg38_GRCh38_v2.3.0.gff3" annotate_cnv: - cnv_amp_genes: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes_hg38.bed" + cnv_amp_genes: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes_hg38_230307.bed" cnv_loh_genes_validated: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_loh_uppsala_genes_hg38.bed" cnv_loh_genes_all: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_loh_genes_hg38.bed" @@ -57,7 +57,7 @@ call_small_cnv_deletions: regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_deletion_genes_hg38.tsv" call_small_cnv_amplifications: - regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amplification_genes_hg38.tsv" + regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amplification_genes_hg38_240307.tsv" cnvkit_batch: normal_reference: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_nextseq_noUmea_27_hg38.cnn" From 46aef96bf47f0f5d17b5c18b8994a49c1cd905c4 Mon Sep 17 00:00:00 2001 From: jonca79 <54137490+jonca79@users.noreply.github.com> Date: Fri, 19 Apr 2024 09:55:10 +0200 Subject: [PATCH 26/40] fix: spelling error --- config/config.data.hg38.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/config.data.hg38.yaml b/config/config.data.hg38.yaml index 15cb0881..f7d341b6 100644 --- a/config/config.data.hg38.yaml +++ b/config/config.data.hg38.yaml @@ -30,7 +30,7 @@ arriba_draw_fusion: protein_domains: "{{PROJECT_REF_DATA}}/ref_data/arriba_v2.3.0/protein_domains_hg38_GRCh38_v2.3.0.gff3" annotate_cnv: - cnv_amp_genes: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes_hg38_230307.bed" + cnv_amp_genes: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes_hg38_240307.bed" cnv_loh_genes_validated: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_loh_uppsala_genes_hg38.bed" cnv_loh_genes_all: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_loh_genes_hg38.bed" From 5e057e78889ce3e6d331704ca123e6fb660c85d1 Mon Sep 17 00:00:00 2001 From: jonca79 <54137490+jonca79@users.noreply.github.com> Date: Fri, 19 Apr 2024 10:21:37 +0200 Subject: [PATCH 27/40] feat: updated with new reference files --- config/references/design_files.hg19.yaml | 27 ++++++++++++++++++------ 1 file changed, 20 insertions(+), 7 deletions(-) diff --git a/config/references/design_files.hg19.yaml b/config/references/design_files.hg19.yaml index 82a6ffef..fb6da1d7 100644 --- a/config/references/design_files.hg19.yaml +++ b/config/references/design_files.hg19.yaml @@ -2,10 +2,10 @@ annotate_cnv: cnv_amp_genes: - path: GMS560/cnv/cnv_amp_genes.bed - checksum: 7bae2d8c592e54207c4b8effaca2bf4f + path: GMS560/cnv/cnv_amp_genes_240307.bed + checksum: daa4bd789c9beb84bf1c02e125dd1fd6 type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.1/cnv/cnv_amp_genes.bed + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.6.0/cnv/cnv_amp_genes_240307.bed cnv_loh_genes_all: path: GMS560/cnv/cnv_loh_genes.bed @@ -42,10 +42,10 @@ call_small_cnv_amplifications: regions_file: - checksum: 24447a09e6691ca7382f4400b06943cf - path: GMS560/cnv/cnv_amplification_genes.tsv + checksum: d276c7848ed8fecc034f76bfd815e537 + path: GMS560/cnv/cnv_amplification_genes_240307.tsv type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.1/cnv/cnv_amplification_genes.tsv + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.6.0/cnv/cnv_amplification_genes_240307.tsv call_small_cnv_deletions: regions_file: @@ -54,6 +54,20 @@ type: file url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.1/cnv/cnv_deletion_genes.tsv + cnvkit_build_normal_reference: + mappability: + checksum: 5663ce9e7576e8ed7b4fa06fad1fdb88 + path: GMS560/cnv/access-5k-mappable.hg19.bed + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.6.0/cnv/access-5k-mappable.hg19.bed + + cnv_tsv_report: + chrom_arm_size: + checksum: 3b0242bea88285383dbb42aec1f252d0 + path: GMS560/cnv/chromosome_arm_size.tsv + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.6.0/cnv/chromosome_arm_size.tsv + exon_skipping: design_bed: checksum: 7fe64299477aa4b6a5f5783cce9fa30f @@ -79,7 +93,6 @@ path: GMS560/fuseq_wes/false_positive_fusion_pairs.txt type: file url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.4.0/fuseq_wes/false_positive_fusion_pairs.txt - fuseq_wes: params: From 0ad022c8f2513a5e0becbe967aff0c2d11c2a86f Mon Sep 17 00:00:00 2001 From: jonca79 <54137490+jonca79@users.noreply.github.com> Date: Fri, 19 Apr 2024 10:24:59 +0200 Subject: [PATCH 28/40] feat: update ref files for hg38 --- config/references/design_files.hg38.yaml | 26 ++++++++++++++++++------ 1 file changed, 20 insertions(+), 6 deletions(-) diff --git a/config/references/design_files.hg38.yaml b/config/references/design_files.hg38.yaml index 69c0318f..644e6a65 100644 --- a/config/references/design_files.hg38.yaml +++ b/config/references/design_files.hg38.yaml @@ -2,10 +2,10 @@ annotate_cnv: cnv_amp_genes: - path: GMS560/cnv/cnv_amp_genes_hg38.bed - checksum: 51ca611484f5b406edfe79f06e8879ef + path: GMS560/cnv/cnv_amp_genes_hg38_240307.bed + checksum: d808ff25722e43a243aa09f2607bc37e type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/cnv_amp_genes_hg38.bed + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.6.0/cnv/cnv_amp_genes_hg38_240307.bed cnv_loh_genes_all: path: GMS560/cnv/cnv_loh_genes_hg38.bed @@ -42,10 +42,10 @@ call_small_cnv_amplifications: regions_file: - checksum: 4f7b0d50c0acc18201512e59322c144c - path: GMS560/cnv/cnv_amplification_genes_hg38.tsv + checksum: 75f7fd3a5e3b9b09935f17ec3d71f6f9 + path: GMS560/cnv/cnv_amplification_genes_hg38_240307.tsv type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/cnv_amplification_genes_hg38.tsv + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/cnv_amplification_genes_hg38_240307.tsv call_small_cnv_deletions: regions_file: @@ -54,6 +54,20 @@ type: file url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/cnv_deletion_genes_hg38.tsv + cnvkit_build_normal_reference: + mappability: + checksum: 1fdacc8565eb13c53580f6c78b953ce5 + path: GMS560/cnv/access-excludes.hg38.bed + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.6.0/cnv/access-excludes.hg38.bed + + cnv_tsv_report: + chrom_arm_size: + checksum: 3b0242bea88285383dbb42aec1f252d0 + path: GMS560/cnv/chromosome_arm_size.tsv + type: file + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.6.0/cnv/chromosome_arm_size.tsv + exon_skipping: design_bed: checksum: 75299f3690fd91d8e42e7db3743896b2 From f8d69e7975f781c63b8fa57fb77b89b0f643cd17 Mon Sep 17 00:00:00 2001 From: Patrik Smeds Date: Fri, 19 Apr 2024 10:40:15 +0200 Subject: [PATCH 29/40] refactor: move chrom arm file --- config/config.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/config/config.yaml b/config/config.yaml index 95d43dfc..1aedaa69 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -90,7 +90,6 @@ cnv_html_report: cnv_tsv_report: amp_cn_limit: 6.0 baseline_fraction_limit: 0.2 - chrom_arm_size: "{{PROJECT_DESIGN_DATA}}/GMS560/design/chromosome_arm_size.tsv" del_1p19q_cn_limit: 1.4 del_1p19q_chr_arm_fraction: 0.3 chr_arm_fraction: 0.3 From 4dd24f21ead2ee24ffb6242a47ef8021c61f6b78 Mon Sep 17 00:00:00 2001 From: Patrik Smeds Date: Fri, 19 Apr 2024 10:42:03 +0200 Subject: [PATCH 30/40] Update config.data.hg19.yaml --- config/config.data.hg19.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/config/config.data.hg19.yaml b/config/config.data.hg19.yaml index e4b2e68a..a15ac3c4 100644 --- a/config/config.data.hg19.yaml +++ b/config/config.data.hg19.yaml @@ -65,6 +65,9 @@ cnvkit_batch: cnvkit_batch_hrd: normal_reference_hrd: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_nextseq_27_HRD.cnn" +cnv_tsv_report: + chrom_arm_size: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/chromosome_arm_size.tsv" + exon_skipping: design_bed: "{{PROJECT_DESIGN_DATA}}/GMS560/design/Twist_RNA_Design5.annotated.bed" From acf3871e8fe501c7c7b9da280049a1fa67cab576 Mon Sep 17 00:00:00 2001 From: Patrik Smeds Date: Fri, 19 Apr 2024 10:42:30 +0200 Subject: [PATCH 31/40] Update config.data.hg38.yaml --- config/config.data.hg38.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/config/config.data.hg38.yaml b/config/config.data.hg38.yaml index f7d341b6..3ffc1ef3 100644 --- a/config/config.data.hg38.yaml +++ b/config/config.data.hg38.yaml @@ -65,6 +65,9 @@ cnvkit_batch: cnvkit_batch_hrd: normal_reference_hrd: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_nextseq_noUmea_27_hg38.cnn" +cnv_tsv_report: + chrom_arm_size: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/chromosome_arm_size.tsv" + exon_skipping: design_bed: "{{PROJECT_DESIGN_DATA}}/GMS560/design/Twist_RNA_Design5.annotated.hg38.bed" From 36b3b0a1eb61ec8416cd90601c08ae957a44e22d Mon Sep 17 00:00:00 2001 From: Patrik Smeds Date: Fri, 19 Apr 2024 14:00:39 +0200 Subject: [PATCH 32/40] fix: correct missing part of vep ref file path --- config/references/references.hg19.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/config/references/references.hg19.yaml b/config/references/references.hg19.yaml index 3468f8c7..d930ed16 100644 --- a/config/references/references.hg19.yaml +++ b/config/references/references.hg19.yaml @@ -389,9 +389,9 @@ path: ref_data/vep/105/homo_sapiens_refseq type: folder content_checksum: - 105_GRCh37/HG1463_PATCH/114000001-115000000_reg.gz: c01d9c84f552841842da29450cbe3e9f + homo_sapiens_refseq/105_GRCh37/HG1463_PATCH/114000001-115000000_reg.gz: c01d9c84f552841842da29450cbe3e9f homo_sapiens_refseq/105_GRCh37/HG1463_PATCH/all_vars.gz: 7a6c597ec65c982c80fe0ab89a071d59 - /105_GRCh37/HG1463_PATCH/114000001-115000000.gz: 876549f369d9c55811216e29f7d0cd19 + homo_sapiens_refseq/105_GRCh37/HG1463_PATCH/114000001-115000000.gz: 876549f369d9c55811216e29f7d0cd19 homo_sapiens_refseq/105_GRCh37/HG1463_PATCH/115000001-116000000_reg.gz: 49865f8fa24479ca5342ce7df5b082d0 homo_sapiens_refseq/105_GRCh37/HG1463_PATCH/all_vars.gz.csi: 66f720e01f5b9f4fefd97225e590aa7c homo_sapiens_refseq/105_GRCh37/HG1463_PATCH/115000001-116000000.gz: bf658fd769d3abd02c07be1538505e36 From 3a2cae4c773f5f8d4ec5ec28f1bfc8f1fcb6c723 Mon Sep 17 00:00:00 2001 From: jonca79 <54137490+jonca79@users.noreply.github.com> Date: Fri, 19 Apr 2024 14:33:28 +0200 Subject: [PATCH 33/40] fix: rm duplicate entries of cnv in report --- workflow/scripts/cnv_report.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/workflow/scripts/cnv_report.py b/workflow/scripts/cnv_report.py index 54784d2d..e4855c75 100644 --- a/workflow/scripts/cnv_report.py +++ b/workflow/scripts/cnv_report.py @@ -138,8 +138,8 @@ def create_tsv_report( gene_all_dict[gene].append([chr, start, end, caller, cn, AF]) else: duplicate = False - for variant in gene_all_dict[gene]: - if chr == variant[0] and start == variant[1] and end == variant[2] and caller == variant[3]: + for cnv_variant in gene_all_dict[gene]: + if chr == cnv_variant[0] and start == cnv_variant[1] and end == cnv_variant[2] and caller == cnv_variant[3]: duplicate = True break if not duplicate: @@ -190,13 +190,13 @@ def create_tsv_report( gene_variant_dict[gene].append([chr, start, end, caller, cn, AF]) for gene in gene_variant_dict: if len(gene_variant_dict[gene]) == 1: - caller = gene_variant_dict[gene][0][3] + org_caller = gene_variant_dict[gene][0][3] for cnv in gene_all_dict[gene]: - if cnv[3] != caller: + if cnv[3] != org_caller: chr = cnv[0] start = cnv[1] end = cnv[2] - caller = cnv[3] + new_caller = cnv[3] cn = cnv[4] AF = cnv[5] if ( @@ -205,7 +205,7 @@ def create_tsv_report( (gene_variant_dict[gene][0][1] >= start and gene_variant_dict[gene][0][1] <= end) or (gene_variant_dict[gene][0][2] >= end and gene_variant_dict[gene][0][2] <= start) ): - writer.write(f"\n{samples}\t{gene}\t{chr}\t{start}-{end}\t{caller}\t{AF:.2f}\t{cn:.2f}") + writer.write(f"\n{samples}\t{gene}\t{chr}\t{start}-{end}\t{new_caller}\t{AF:.2f}\t{cn:.2f}") log.info(f"Processed {counter} variants") deletions = open(input_del) From e8efb8c2162cbb71df1c3ab01ed7c26e28e411a9 Mon Sep 17 00:00:00 2001 From: Patrik Smeds Date: Fri, 19 Apr 2024 14:38:47 +0200 Subject: [PATCH 34/40] fix: update hg38 ref files, point to correct release --- config/references/design_files.hg38.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/references/design_files.hg38.yaml b/config/references/design_files.hg38.yaml index 644e6a65..475d0b60 100644 --- a/config/references/design_files.hg38.yaml +++ b/config/references/design_files.hg38.yaml @@ -45,7 +45,7 @@ checksum: 75f7fd3a5e3b9b09935f17ec3d71f6f9 path: GMS560/cnv/cnv_amplification_genes_hg38_240307.tsv type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/cnv_amplification_genes_hg38_240307.tsv + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.6.0/cnv/cnv_amplification_genes_hg38_240307.tsv call_small_cnv_deletions: regions_file: From 6dc14a9dff4df0d9277cb8bab2013841cc47b848 Mon Sep 17 00:00:00 2001 From: jonca79 <54137490+jonca79@users.noreply.github.com> Date: Fri, 19 Apr 2024 14:38:51 +0200 Subject: [PATCH 35/40] chore: pycodestyle --- workflow/scripts/cnv_report.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/workflow/scripts/cnv_report.py b/workflow/scripts/cnv_report.py index e4855c75..c57734a7 100644 --- a/workflow/scripts/cnv_report.py +++ b/workflow/scripts/cnv_report.py @@ -139,7 +139,10 @@ def create_tsv_report( else: duplicate = False for cnv_variant in gene_all_dict[gene]: - if chr == cnv_variant[0] and start == cnv_variant[1] and end == cnv_variant[2] and caller == cnv_variant[3]: + if ( + chr == cnv_variant[0] and start == cnv_variant[1] and + end == cnv_variant[2] and caller == cnv_variant[3] + ): duplicate = True break if not duplicate: From e616490e5db557becbab1eb5bf5910b5860812af Mon Sep 17 00:00:00 2001 From: jonca79 <54137490+jonca79@users.noreply.github.com> Date: Fri, 19 Apr 2024 14:40:43 +0200 Subject: [PATCH 36/40] chore: pycodestyle --- workflow/scripts/cnv_report.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/scripts/cnv_report.py b/workflow/scripts/cnv_report.py index c57734a7..7bb000e0 100644 --- a/workflow/scripts/cnv_report.py +++ b/workflow/scripts/cnv_report.py @@ -140,7 +140,7 @@ def create_tsv_report( duplicate = False for cnv_variant in gene_all_dict[gene]: if ( - chr == cnv_variant[0] and start == cnv_variant[1] and + chr == cnv_variant[0] and start == cnv_variant[1] and end == cnv_variant[2] and caller == cnv_variant[3] ): duplicate = True From be98e22671d1f31d684d4ea45294d7b89f0aa55f Mon Sep 17 00:00:00 2001 From: Patrik Smeds Date: Mon, 22 Apr 2024 13:06:31 +0200 Subject: [PATCH 37/40] fix: update config, merge_cnv_json, to use latest amp gene bed file --- config/config.data.hg19.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/config.data.hg19.yaml b/config/config.data.hg19.yaml index a15ac3c4..2825fd0e 100644 --- a/config/config.data.hg19.yaml +++ b/config/config.data.hg19.yaml @@ -117,7 +117,7 @@ manta_config_t: merge_cnv_json: annotations: - - "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes.bed" + - "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes_240307.bed" - "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_loh_genes.bed" mosdepth: From 36bab94d269fc31a756e2f211de78afe512173a0 Mon Sep 17 00:00:00 2001 From: Patrik Smeds Date: Wed, 24 Apr 2024 14:49:08 +0200 Subject: [PATCH 38/40] feat: update test file for develop --- .tests/jenkins/test_input_develop.tsv | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.tests/jenkins/test_input_develop.tsv b/.tests/jenkins/test_input_develop.tsv index b6014830..7e1a05f8 100644 --- a/.tests/jenkins/test_input_develop.tsv +++ b/.tests/jenkins/test_input_develop.tsv @@ -6,13 +6,13 @@ results/dna/VAL2022-2-5M_T/additional_files/biomarker/VAL2022-2-5M_T.purecn.scar results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.amplifications.tsv f397f92f69100d1f20ca65ffac830dd0 results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.deletions.tsv f887194ae8134c8a1c8fd427ae533646 results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.manta_tumorSV.vcf.gz 1c4f0a2b346d1355dc76fcd126222729 -results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.amp_all_del_all.cnv_report.tsv 831ba945efe70a4fe5df10d632a017ce -results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.amp_all_del_validated.cnv_report.tsv 63fb792a3010418b15c5971d402886ac -results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology_purecn.amp_all_del_all.cnv_report.tsv aebb2658c6c2112c29ffbd710e5a9d77 +results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.amp_all_del_all.cnv_report.tsv 0391e5f6f8bd9b24d3bb390834078235 +results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.amp_all_del_validated.cnv_report.tsv 1872cc3c11c4af3e214dccdbca653460 +results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology_purecn.amp_all_del_all.cnv_report.tsv 8a85c32ff5b4e0668376043e16dc0e77 results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology_purecn.svdb_query.vcf c5ebcc72790e0c6f5186298bf5890348 results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.svdb_query.vcf c51a58f9332c9176b0f354a955fd25bc -results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.amp_all_del_all.cnv_report.tsv aebb2658c6c2112c29ffbd710e5a9d77 -results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.amp_all_del_validated.cnv_report.tsv 73e862d949f8de401c23170ca6db09d4 +results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.amp_all_del_all.cnv_report.tsv 8a85c32ff5b4e0668376043e16dc0e77 +results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.amp_all_del_validated.cnv_report.tsv 2438c93ab15eb0e2f6595ac5c006a1f2 results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.svdb_query.vcf 49498b22ca7af9176b31e194ef5eb42f results/dna/VAL2022-2-5M_T/additional_files/qc/VAL2022-2-5M_T.alignment_summary_metrics.txt fa88f8adc1d6146cf399c6d17a37d098 results/dna/VAL2022-2-5M_T/additional_files/qc/VAL2022-2-5M_T.contamination.table a4ee6cd2e1cfe029229f5b218ac318e9 @@ -28,7 +28,7 @@ results/dna/VAL2022-2-5M_T/additional_files/vcf/vardict_VAL2022-2-5M_T.vcf.gz 22 results/dna/VAL2022-2-5M_T/biomarker/VAL2022-2-5M_T.msisensor_pro.score.tsv e47f1fb00f0220a20335f972e1af8d39 results/dna/VAL2022-2-5M_T/biomarker/VAL2022-2-5M_T.pathology_purecn.scarhrd_cnvkit_score.txt 55145eab2e60e588c66b233cf1479287 results/dna/VAL2022-2-5M_T/biomarker/VAL2022-2-5M_T.TMB.txt e20d98b80deb3ad74605c0439abda1f2 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100644 --- a/.tests/jenkins/test_input_develop.tsv +++ b/.tests/jenkins/test_input_develop.tsv @@ -6,8 +6,8 @@ results/dna/VAL2022-2-5M_T/additional_files/biomarker/VAL2022-2-5M_T.purecn.scar results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.amplifications.tsv f397f92f69100d1f20ca65ffac830dd0 results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.deletions.tsv f887194ae8134c8a1c8fd427ae533646 results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.manta_tumorSV.vcf.gz 1c4f0a2b346d1355dc76fcd126222729 -results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.amp_all_del_all.cnv_report.tsv 0391e5f6f8bd9b24d3bb390834078235 -results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.amp_all_del_validated.cnv_report.tsv 1872cc3c11c4af3e214dccdbca653460 +results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.amp_all_del_all.cnv_report.tsv 2b09144044b2bdf63c440082be760b26 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