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Add AIVariant tumor-normal caller with chromosome chunking #12

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8 changes: 4 additions & 4 deletions .test_data/data/0.01x_3_wgs_HG002_hg38.samplesheet.csv
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samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,external_sample_id,instrument,lib_prep,bwa_kmer,subsample_pct
RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,HG002,NOVASEQ,PCR-FREE,19,0.95
RIH0_ANA0-HG002_DBC1_0,RIH0_ANA0-HG002_DBC1_2,RIH0_ANA0-HG002_DBC1_2,DBC2,RIH0,ANA0-HG002,2,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,HG002,NOVASEQ,PCR-FREE,19,0.85
RIH0_ANA0-HG002_DBC1_0,RIH0_ANA0-HG002_DBC1_1,RIH0_ANA0-HG002_DBC1_1,DBC1,RIH0,ANA0-HG002,1,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,HG002,NOVASEQ,PCR-FREE,19,0.75
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,external_sample_id,tum_nrm_sampleid_match,instrument,lib_prep,bwa_kmer,subsample_pct
RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19,0.95
RIH0_ANA0-HG002_DBC1_0,RIH0_ANA0-HG002_DBC1_2,RIH0_ANA0-HG002_DBC1_2,DBC2,RIH0,ANA0-HG002,2,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19,0.85
RIH0_ANA0-HG002_DBC1_0,RIH0_ANA0-HG002_DBC1_1,RIH0_ANA0-HG002_DBC1_1,DBC1,RIH0,ANA0-HG002,1,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19,0.75
4 changes: 2 additions & 2 deletions .test_data/data/0.01xwgs_HG002_b37.samplesheet.csv
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@@ -1,2 +1,2 @@
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,external_sample_id,instrument,lib_prep,bwa_kmer
RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,NOVASEQ,PCR-FREE,19
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,external_sample_id,tum_nrm_sampleid_match,instrument,lib_prep,bwa_kmer
RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19
4 changes: 2 additions & 2 deletions .test_data/data/0.01xwgs_HG002_hg38.samplesheet.csv
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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,external_sample_id,instrument,lib_prep,bwa_kmer
RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,HG002,NOVASEQ,PCR-FREE,19
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,external_sample_id,tum_nrm_sampleid_match,instrument,lib_prep,bwa_kmer
RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19
16 changes: 8 additions & 8 deletions .test_data/data/giab_30x_b37_analysis_manifest.csv
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,external_sample_id,instrument,lib_prep,bwa_kmer
R0_HG001_D0_0,R0_HG001_D0_0,R0_HG001_D0_0,D0,R0,HG001,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG001/,true,false,blood,merge,HG001,NOVASEQ,PCR-FREE,19
R0_HG002_D0_0,R0_HG002_D0_0,R0_HG002_D0_0,D0,R0,HG002,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,NOVASEQ,PCR-FREE,19
R0_HG003_D0_0,R0_HG003_D0_0,R0_HG003_D0_0,D0,R0,HG003,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG003/,true,false,blood,merge,HG003,NOVASEQ,PCR-FREE,19
R0_HG004_D0_0,R0_HG004_D0_0,R0_HG004_D0_0,D0,R0,HG004,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG004/,true,false,blood,merge,HG004,NOVASEQ,PCR-FREE,19
R0_HG005_D0_0,R0_HG005_D0_0,R0_HG005_D0_0,D0,R0,HG005,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG005/,true,false,blood,merge,HG005,NOVASEQ,PCR-FREE,19
R0_HG006_D0_0,R0_HG006_D0_0,R0_HG006_D0_0,D0,R0,HG006,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG006/,true,false,blood,merge,HG006,NOVASEQ,PCR-FREE,19
R0_HG007_D0_0,R0_HG007_D0_0,R0_HG007_D0_0,D0,R0,HG007,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG007/,true,false,blood,merge,HG007,NOVASEQ,PCR-FREE,19
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,external_sample_id,tum_nrm_sampleid_match,instrument,lib_prep,bwa_kmer
R0_HG001_D0_0,R0_HG001_D0_0,R0_HG001_D0_0,D0,R0,HG001,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG001/,true,false,blood,merge,HG001,HG001,NOVASEQ,PCR-FREE,19
R0_HG002_D0_0,R0_HG002_D0_0,R0_HG002_D0_0,D0,R0,HG002,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19
R0_HG003_D0_0,R0_HG003_D0_0,R0_HG003_D0_0,D0,R0,HG003,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG003/,true,false,blood,merge,HG003,HG003,NOVASEQ,PCR-FREE,19
R0_HG004_D0_0,R0_HG004_D0_0,R0_HG004_D0_0,D0,R0,HG004,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG004/,true,false,blood,merge,HG004,HG004,NOVASEQ,PCR-FREE,19
R0_HG005_D0_0,R0_HG005_D0_0,R0_HG005_D0_0,D0,R0,HG005,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG005/,true,false,blood,merge,HG005,HG005,NOVASEQ,PCR-FREE,19
R0_HG006_D0_0,R0_HG006_D0_0,R0_HG006_D0_0,D0,R0,HG006,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG006/,true,false,blood,merge,HG006,HG006,NOVASEQ,PCR-FREE,19
R0_HG007_D0_0,R0_HG007_D0_0,R0_HG007_D0_0,D0,R0,HG007,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG007/,true,false,blood,merge,HG007,HG007,NOVASEQ,PCR-FREE,19
16 changes: 8 additions & 8 deletions .test_data/data/giab_30x_hg38_analysis_manifest.csv
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,external_sample_id,instrument,lib_prep,bwa_kmer
R0_HG001_D0_0,R0_HG001_D0_0,R0_HG001_D0_0,D0,R0,HG001,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG001/,true,false,blood,merge,HG001,NOVASEQ,PCR-FREE,19
R0_HG002_D0_0,R0_HG002_D0_0,R0_HG002_D0_0,D0,R0,HG002,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,NOVASEQ,PCR-FREE,19
R0_HG003_D0_0,R0_HG003_D0_0,R0_HG003_D0_0,D0,R0,HG003,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/,true,false,blood,merge,HG003,NOVASEQ,PCR-FREE,19
R0_HG004_D0_0,R0_HG004_D0_0,R0_HG004_D0_0,D0,R0,HG004,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG004/,true,false,blood,merge,HG004,NOVASEQ,PCR-FREE,19
R0_HG005_D0_0,R0_HG005_D0_0,R0_HG005_D0_0,D0,R0,HG005,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG005/,true,false,blood,merge,HG005,NOVASEQ,PCR-FREE,19
R0_HG006_D0_0,R0_HG006_D0_0,R0_HG006_D0_0,D0,R0,HG006,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG006/,true,false,blood,merge,HG006,NOVASEQ,PCR-FREE,19
R0_HG007_D0_0,R0_HG007_D0_0,R0_HG007_D0_0,D0,R0,HG007,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG007/,true,false,blood,merge,HG007,NOVASEQ,PCR-FREE,19
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,external_sample_id,tum_nrm_sampleid_match,instrument,lib_prep,bwa_kmer
R0_HG001_D0_0,R0_HG001_D0_0,R0_HG001_D0_0,D0,R0,HG001,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG001/,true,false,blood,merge,HG001,HG001,NOVASEQ,PCR-FREE,19
R0_HG002_D0_0,R0_HG002_D0_0,R0_HG002_D0_0,D0,R0,HG002,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19
R0_HG003_D0_0,R0_HG003_D0_0,R0_HG003_D0_0,D0,R0,HG003,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/,true,false,blood,merge,HG003,HG003,NOVASEQ,PCR-FREE,19
R0_HG004_D0_0,R0_HG004_D0_0,R0_HG004_D0_0,D0,R0,HG004,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG004/,true,false,blood,merge,HG004,HG004,NOVASEQ,PCR-FREE,19
R0_HG005_D0_0,R0_HG005_D0_0,R0_HG005_D0_0,D0,R0,HG005,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG005/,true,false,blood,merge,HG005,HG005,NOVASEQ,PCR-FREE,19
R0_HG006_D0_0,R0_HG006_D0_0,R0_HG006_D0_0,D0,R0,HG006,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG006/,true,false,blood,merge,HG006,HG006,NOVASEQ,PCR-FREE,19
R0_HG007_D0_0,R0_HG007_D0_0,R0_HG007_D0_0,D0,R0,HG007,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG007/,true,false,blood,merge,HG007,HG007,NOVASEQ,PCR-FREE,19
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