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Test data replacement addition chart
GCJMackenzie edited this page Nov 30, 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_snpeff.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_snpeff.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_snpeff.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_snpeff.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 |
| Somatic: | |||||
| 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 |
| Reference: | |||||
| hg38_chr21.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 |
| hg38_chr21.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 |
| hg38_chr21.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 |
| hg38_chr21.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 |
| hg38_chr21.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 |
| hg38_chr21.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 |
| hg38_chr21.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 |
| hg38_chr21.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 |
| hg38_chr21.1.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 |
| hg38_chr21.2.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 |
| hg38_chr21.3.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 |
| hg38_chr21.4.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 |
| hg38_chr21.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 |
| hg38_chr21.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 |
| 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 |