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Test data replacement addition chart
GCJMackenzie edited this page Dec 8, 2021
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13 revisions
| New File Name: | Source File Name: | Replacing file: | description: | repo-location | Source File origin: |
|---|---|---|---|---|---|
| Germline: | |||||
| test2.recal | test.recal | New File | Recalibration table output from VariantRecalibrator, used by ApplyVQSR | data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/ | https://github.com/GCJMackenzie/test_data/tree/master/vrecals_base |
| test2.recal.idx | test.recal.idx | New File | Recalibration table index output from VariantRecalibrator, used by ApplyVQSR | data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/ | https://github.com/GCJMackenzie/test_data/tree/master/vrecals_base |
| test2.tranches | test.tranches | New File | Recalibration table tranches output from VariantRecalibrator, used by ApplyVQSR | data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/ | https://github.com/GCJMackenzie/test_data/tree/master/vrecals_base |
| test2_allele_specific.recal | test_allele_specific.recal | New File | Allele specific Recalibration table output from VariantRecalibrator, used by ApplyVQSR | data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/ | https://github.com/GCJMackenzie/test_data/blob/master/vrecals_as/ |
| test2_allele_specific.recal.idx | test_allele_specific.recal.idx | New File | Allele specific Recalibration table index output from VariantRecalibrator, used by ApplyVQSR | data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/ | https://github.com/GCJMackenzie/test_data/blob/master/vrecals_as/ |
| test2_allele_specific.tranches | test_allele_specific.tranches | New File | Allele specific Recalibration table tranches output from VariantRecalibrator, used by ApplyVQSR | data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/ | https://github.com/GCJMackenzie/test_data/blob/master/vrecals_as/ |
| test2_germline_1.fq.gz | normal_0.000+disease_1.000_1.fq.gz | New File | Synthetic raw reads file used to generate disease test data for HaplotypeCaller | data/genomics/homo_sapiens/illumina/fastq/ | https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/reads/ |
| test2_germline_2.fq.gz | normal_0.000+disease_1.000_2.fq.gz | New File | Synthetic raw reads file used to generate disease test data for HaplotypeCaller | data/genomics/homo_sapiens/illumina/fastq/ | https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/reads/ |
| test_germline_1.fq.gz | normal_1.000+disease_0.000_1.fq.gz | New File | Synthetic raw reads file used to generate normal test data for HaplotypeCaller | data/genomics/homo_sapiens/illumina/fastq/ | https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/reads/ |
| test_germline_2.fq.gz | normal_1.000+disease_0.000_2.fq.gz | New File | Synthetic raw reads file used to generate normal test data for HaplotypeCaller | data/genomics/homo_sapiens/illumina/fastq/ | https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/reads/ |
| test2_haplotc.vcf.gz | HaplotypeCaller_disease_103.vcf.gz | New File | vcf output from HaplotypeCaller using germline disease reads | data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/ | https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/variants |
| test2_haplotc.vcf.gz.tbi | HaplotypeCaller_disease_103.vcf.gz.tbi | New File | vcf.tbi output from HaplotypeCaller using germline disease reads | data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/ | https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/variants |
| test_haplotc.vcf.gz | HaplotypeCaller_normal.vcf.gz | New File | vcf output from HaplotypeCaller using germline normal reads | data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/ | https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/variants |
| test_haplotc.vcf.gz.tbi | HaplotypeCaller_normal.vcf.gz.tbi | New File | vcf.tbi output from HaplotypeCaller using germline normal reads | data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/ | https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/variants |
| test2_haplotc.ann.vcf.gz | HaplotypeCaller_disease_103_snpEff.ann.vcf.gz | New File | vcf output from HaplotypeCaller using germline disease reads annotated using snpEff | data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/ | https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/variants |
| test2_haplotc.ann.vcf.gz.tbi | HaplotypeCaller_disease_103_snpEff.ann.vcf.gz.tbi | New File | vcf.tbi output from HaplotypeCaller using germline disease reads annotated using snpEff | data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/ | https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/variants |
| test_haplotc.ann.vcf.gz | HaplotypeCaller_normal_snpEff.ann.vcf.gz | New File | vcf output from HaplotypeCaller using germline normal reads annotated using snpEff | data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/ | https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/variants |
| test_haplotc.ann.vcf.gz.tbi | HaplotypeCaller_normal_snpEff.ann.vcf.gz.tbi | New File | vcf.tbi output from HaplotypeCaller using germline normal reads annotated using snpEff | data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/ | https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/variants |
| test.g.vcf.gz | test.g.vcf.gz | New File | output from haplotypecaller run in GVCF mode using germline normal sample | data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/ | Local run of gatk_joint_germline_variant_calling subworkflow |
| test.g.vcf.gz.tbi | test.g.vcf.gz.tbi | New File | output index from haplotypecaller run in GVCF mode using germline normal sample | data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/ | Local run of gatk_joint_germline_variant_calling subworkflow |
| test2.g.vcf.gz | test2.g.vcf.gz | New File | output from haplotypecaller run in GVCF mode using germline diesease sample | data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/ | Local run of gatk_joint_germline_variant_calling subworkflow |
| test2.g.vcf.gz.tbi | test2.g.vcf.gz.tbi | New File | output index from haplotypecaller run in GVCF mode using germline disease sample | data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/ | Local run of gatk_joint_germline_variant_calling subworkflow |
| Somatic: | |||||
| Cram file equivalents also added for each of the following bam files | |||||
| test2.paired_end.recalibrated.sorted.bam | tumour.recal.bam | test2.paired_end.recalibrated.sorted.bam | recalibrated bam file of tumor reads | data/genomics/homo_sapiens/illumina/bam/ | https://github.com/GCJMackenzie/datasets_class/tree/master/somatic_calling/alignments |
| test.paired_end.recalibrated.sorted.bam | normal.recal.bam | test.paired_end.recalibrated.sorted.bam | recalibrated bam file of normal reads | data/genomics/homo_sapiens/illumina/bam/ | https://github.com/GCJMackenzie/datasets_class/tree/master/somatic_calling/alignments |
| test2.paired_end.recalibrated.sorted.bam.bai | tumour.recal.bam.bai | test2.paired_end.recalibrated.sorted.bam.bai | recalibrated bam index of tumor reads | data/genomics/homo_sapiens/illumina/bam/ | https://github.com/GCJMackenzie/datasets_class/tree/master/somatic_calling/alignments |
| test.paired_end.recalibrated.sorted.bam.bai | normal.recal.bam.bai | test.paired_end.recalibrated.sorted.bam.bai | recalibrated bam index of normal reads | data/genomics/homo_sapiens/illumina/bam/ | https://github.com/GCJMackenzie/datasets_class/tree/master/somatic_calling/alignments |
| test2.paired_end.markduplicates.sorted.bam | tumour.md.bam | test2.paired_end.markduplicates.sorted.bam | bam file of tumor reads with duplicates marked | data/genomics/homo_sapiens/illumina/bam/ | https://github.com/GCJMackenzie/datasets_class/tree/master/somatic_calling/alignments |
| test.paired_end.markduplicates.sorted.bam | normal.md.bam | test.paired_end.markduplicates.sorted.bam | bam file of normal reads with duplicates marked | data/genomics/homo_sapiens/illumina/bam/ | https://github.com/GCJMackenzie/datasets_class/tree/master/somatic_calling/alignments |
| test2.paired_end.markduplicates.sorted.bam.bai | tumour.md.bam.bai | test2.paired_end.markduplicates.sorted.bam.bai | bam index of tumor reads with duplicates marked | data/genomics/homo_sapiens/illumina/bam/ | https://github.com/GCJMackenzie/datasets_class/tree/master/somatic_calling/alignments |
| test.paired_end.markduplicates.sorted.bam.bai | normal.md.bam.bai | test.paired_end.markduplicates.sorted.bam.bai | bam index of tumor reads with duplicates marked | data/genomics/homo_sapiens/illumina/bam/ | https://github.com/GCJMackenzie/datasets_class/tree/master/somatic_calling/alignments |
| test_1.fastq.gz | normal_1.000+disease_0.000_1.fq.gz | test_1.fastq.gz | Synthetic raw reads file used to generate normal test data for mutect2 | data/genomics/homo_sapiens/illumina/fastq/ | https://github.com/GCJMackenzie/datasets_class/tree/master/somatic_calling/reads |
| test_2.fastq.gz | normal_1.000+disease_0.000_2.fq.gz | test_2.fastq.gz | Synthetic raw reads file used to generate normal test data for mutect2 | data/genomics/homo_sapiens/illumina/fastq/ | https://github.com/GCJMackenzie/datasets_class/tree/master/somatic_calling/reads |
| test2_1.fastq.gz | normal_0.700+disease_0.300_1.fq.gz | test2_1.fastq.gz | Synthetic raw reads file used to generate tumor test data for mutect2 | data/genomics/homo_sapiens/illumina/fastq/ | https://github.com/GCJMackenzie/datasets_class/tree/master/somatic_calling/reads |
| test2_2.fastq.gz | normal_0.700+disease_0.300_2.fq.gz | test2_2.fastq.gz | Synthetic raw reads file used to generate tumor test data for mutect2 | data/genomics/homo_sapiens/illumina/fastq/ | https://github.com/GCJMackenzie/datasets_class/tree/master/somatic_calling/reads |
| test_pon.vcf.gz | test1.vcf.gz | New File | variant calls of normal sample run through mutect2 in panel of normals mode | data/genomics/homo_sapiens/illumina/gatk/pon_mutect2_calls/ | Local run of gatk_create_som_pon subworkflow |
| test_pon.vcf.gz.tbi | test1.vcf.gz.tbi | New File | variant calls tbi of normal sample run through mutect2 in panel of normals mode | data/genomics/homo_sapiens/illumina/gatk/pon_mutect2_calls/ | Local run of gatk_create_som_pon subworkflow |
| test_pon.vcf.gz.stats | test1.vcf.gz.stats | New File | variant calls stats file of normal sample run through mutect2 in panel of normals mode | data/genomics/homo_sapiens/illumina/gatk/pon_mutect2_calls/ | Local run of gatk_create_som_pon subworkflow |
| test2_pon.vcf.gz | test2.vcf.gz | New File | variant calls of tumor sample run through mutect2 in panel of normals mode | data/genomics/homo_sapiens/illumina/gatk/pon_mutect2_calls/ | Local run of gatk_create_som_pon subworkflow |
| test2_pon.vcf.gz.tbi | test2.vcf.gz.tbi | New File | variant calls index of tumor sample run through mutect2 in panel of normals mode | data/genomics/homo_sapiens/illumina/gatk/pon_mutect2_calls/ | Local run of gatk_create_som_pon subworkflow |
| test2_pon.vcf.gz.stats | test2.vcf.gz.stats | New File | variant calls stats file of tumor sample run through mutect2 in panel of normals mode | data/genomics/homo_sapiens/illumina/gatk/pon_mutect2_calls/ | Local run of gatk_create_som_pon subworkflow |
| test_pon_genomicsdb.tar.gz | test_panel/ | test_genomicsdb.tar.gz | genomicsdb workspace made from test_pon and test2_pon vcf files, used to test createsomaticpanelofnormals and genotypegvcfs, this is only useful for tests and is not valid for true panel of normals as it contains tumor sample | data/genomics/homo_sapiens/illumina/gatk/ | Local run of gatk_create_som_pon subworkflow |
| test.pileups.table | test_normal.pileups.table | test.pileups.table | pileups table for normal sample | data/genomics/homo_sapiens/illumina/gatk/ | Local run of gatk_tumor_normal_somatic_variant_calling subworkflow |
| test2.pileups.table | test_tumor.pileups.table | test2.pileups.table | pileups table for tumor sample | data/genomics/homo_sapiens/illumina/gatk/ | Local run of gatk_tumor_normal_somatic_variant_calling subworkflow |
| test_test2_paired_mutect2_calls.artifact-prior.tar.gz | test.tar.gz | test_test2_paired_mutect2_calls.artifact-prior.tar.gz | artifacts prior from learnreadorientationmodel being run on paired tumor normal f1r2 | data/genomics/homo_sapiens/illumina/gatk/ | Local run of gatk_tumor_normal_somatic_variant_calling subworkflow |
| test_test2_paired.contamination.table | test.contamination.table | test_test2_paired.contamination.table | contamination table of paired tumor normal data | data/genomics/homo_sapiens/illumina/gatk/ | Local run of gatk_tumor_normal_somatic_variant_calling subworkflow |
| test_test2_paired.segmentation.table | test.segmentation.table | test_test2_paired.segmentation.table | segmentation data of paired tumor normal data | data/genomics/homo_sapiens/illumina/gatk/ | Local run of gatk_tumor_normal_somatic_variant_calling subworkflow |
| test_test2_paired_mutect2_calls.vcf.gz | test.vcf.gz | test_test2_paired_mutect2_calls.vcf.gz | variant calls for tumor normal paired samples output from mutect2 | data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/ | Local run of gatk_tumor_normal_somatic_variant_calling subworkflow |
| test_test2_paired_mutect2_calls.vcf.gz.tbi | test.vcf.gz.tbi | test_test2_paired_mutect2_calls.vcf.gz.tbi | variant calls tbi for tumor normal paired samples output from mutect2 | data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/ | Local run of gatk_tumor_normal_somatic_variant_calling subworkflow |
| test_test2_paired_mutect2_calls.vcf.gz.stats | test.vcf.gz.stats | test_test2_paired_mutect2_calls.vcf.gz.stats | variant calls stats file for tumor normal paired samples output from mutect2 | data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/ | Local run of gatk_tumor_normal_somatic_variant_calling subworkflow |
| test_test2_paired_mutect2_calls.f1r2.tar.gz | test.f1r2.tar.gz | test_test2_paired_mutect2_calls.f1r2.tar.gz | description: | data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/ | Local run of gatk_tumor_normal_somatic_variant_calling subworkflow |
| test_test2_paired_filtered_mutect2_calls.vcf.gz | test_filtered.vcf.gz | New File | tumor normal vcf file after being passed through filtermutectcalls | data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/ | Local run of gatk_tumor_normal_somatic_variant_calling subworkflow |
| test_test2_paired_filtered_mutect2_calls.vcf.gz.tbi | test_filtered.vcf.gz.tbi | New File | tbi file for the tumor normal vcf file after being passed through filtermutectcalls | data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/ | Local run of gatk_tumor_normal_somatic_variant_calling subworkflow |
| test_test2_paired_filtered_mutect2_calls.vcf.gz.filteringStats.tsv | test_filtered.vcf.gz.filteringStats.tsv | New File | filtering stats file for the tumor normal vcf file after being passed through filtermutectcalls | data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/ | Local run of gatk_tumor_normal_somatic_variant_calling subworkflow |
| mitochon_standin.recalibrated.sorted.bam | test.paired_end.recalibrated.sorted.bam | New File | since we have no mitochondria test data, I have kept this old bam file as a stand in | data/genomics/homo_sapiens/illumina/bam/ | Old test-datasets recalibrated bam |
| mitochon_standin.recalibrated.sorted.bam.bai | test.paired_end.recalibrated.sorted.bam.bai | New File | since we have no mitochondria test data, I have kept this old bam file index as a stand in | data/genomics/homo_sapiens/illumina/bam/ | Old test-datasets recalibrated bam |
| Reference: | |||||
| genome.fasta | Homo_sapiens_assembly38_chr21.fasta | New File | fasta file containing sequence data from chr21 of hg assembly 38 | data/genomics/homo_sapiens/genome/chr21/sequence/ | https://github.com/lescai-teaching/datasets_class/tree/master/reference/sequence |
| genome.fasta.fai | Homo_sapiens_assembly38_chr21.fasta.fai | New File | index/dictionary file | data/genomics/homo_sapiens/genome/chr21/sequence/ | https://github.com/lescai-teaching/datasets_class/tree/master/reference/sequence |
| genome.dict | Homo_sapiens_assembly38_chr21.dict | New File | index/dictionary file | data/genomics/homo_sapiens/genome/chr21/sequence/ | https://github.com/lescai-teaching/datasets_class/tree/master/reference/sequence |
| genome.fasta.pac | Homo_sapiens_assembly38_chr21.fasta.pac | New File | index/dictionary file | data/genomics/homo_sapiens/genome/chr21/sequence/ | https://github.com/lescai-teaching/datasets_class/tree/master/reference/sequence |
| genome.fasta.bwt | Homo_sapiens_assembly38_chr21.fasta.bwt | New File | index/dictionary file | data/genomics/homo_sapiens/genome/chr21/sequence/ | https://github.com/lescai-teaching/datasets_class/tree/master/reference/sequence |
| genome.fasta.amb | Homo_sapiens_assembly38_chr21.fasta.amb | New File | index/dictionary file | data/genomics/homo_sapiens/genome/chr21/sequence/ | https://github.com/lescai-teaching/datasets_class/tree/master/reference/sequence |
| genome.fasta.ann | Homo_sapiens_assembly38_chr21.fasta.ann | New File | index/dictionary file | data/genomics/homo_sapiens/genome/chr21/sequence/ | https://github.com/lescai-teaching/datasets_class/tree/master/reference/sequence |
| genome.fasta.sa | Homo_sapiens_assembly38_chr21.fasta.sa | New File | index/dictionary file | data/genomics/homo_sapiens/genome/chr21/sequence/ | https://github.com/lescai-teaching/datasets_class/tree/master/reference/sequence |
| genome.1.bt2 | Homo_sapiens_assembly38_chr21.1.bt2 | New File | index/dictionary file | data/genomics/homo_sapiens/genome/chr21/sequence/ | https://github.com/lescai-teaching/datasets_class/tree/master/reference/sequence |
| genome.2.bt2 | Homo_sapiens_assembly38_chr21.2.bt2 | New File | index/dictionary file | data/genomics/homo_sapiens/genome/chr21/sequence/ | https://github.com/lescai-teaching/datasets_class/tree/master/reference/sequence |
| genome.3.bt2 | Homo_sapiens_assembly38_chr21.3.bt2 | New File | index/dictionary file | data/genomics/homo_sapiens/genome/chr21/sequence/ | https://github.com/lescai-teaching/datasets_class/tree/master/reference/sequence |
| genome.4.bt2 | Homo_sapiens_assembly38_chr21.4.bt2 | New File | index/dictionary file | data/genomics/homo_sapiens/genome/chr21/sequence/ | https://github.com/lescai-teaching/datasets_class/tree/master/reference/sequence |
| genome.rev.1.bt2 | Homo_sapiens_assembly38_chr21.rev.1.bt2 | New File | index/dictionary file | data/genomics/homo_sapiens/genome/chr21/sequence/ | https://github.com/lescai-teaching/datasets_class/tree/master/reference/sequence |
| genome.rev.2.bt2 | Homo_sapiens_assembly38_chr21.rev.2.bt2 | New File | index/dictionary file | data/genomics/homo_sapiens/genome/chr21/sequence/ | https://github.com/lescai-teaching/datasets_class/tree/master/reference/sequence |
| genome.interval_list | hg38_chr21.interval_list | New File | intervals list file containing 1 interval for all of chr21 | data/genomics/homo_sapiens/genome/chr21/sequence/ | written mannualy |
| germlineresources/ | gatkbundle/ | New Files | subdirectory of 9 germline resources for use with gatk tools (and anything else that uses germline resources in vcf format) | data/genomics/homo_sapiens/genome/chr21/gatkbundle/ | https://github.com/lescai-teaching/datasets_class/tree/master/reference/gatkbundle |