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58 changes: 58 additions & 0 deletions
58
...pshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_ped.snap
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--- | ||
source: src/seqvars/ingest/header.rs | ||
expression: "std::fs::read_to_string(out_path_str)?" | ||
--- | ||
##fileformat=VCFv4.4 | ||
##INFO=<ID=gnomad_exomes_an,Number=1,Type=Integer,Description="Number of samples in gnomAD exomes"> | ||
##INFO=<ID=gnomad_exomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD exomes"> | ||
##INFO=<ID=gnomad_exomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD exomes"> | ||
##INFO=<ID=gnomad_exomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD exomes"> | ||
##INFO=<ID=gnomad_genomes_an,Number=1,Type=Integer,Description="Number of samples in gnomAD genomes"> | ||
##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes"> | ||
##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes"> | ||
##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes"> | ||
##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of samples in HelixMtDb"> | ||
##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb"> | ||
##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb"> | ||
##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'"> | ||
##FILTER=<ID=PASS,Description="All filters passed"> | ||
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele"> | ||
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> | ||
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality"> | ||
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> | ||
##contig=<ID=chr1,length=248956422,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr2,length=242193529,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr3,length=198295559,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr4,length=190214555,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr5,length=181538259,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr6,length=170805979,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr7,length=159345973,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr8,length=145138636,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr9,length=138394717,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr10,length=133797422,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr11,length=135086622,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr12,length=133275309,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr13,length=114364328,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr14,length=107043718,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr15,length=101991189,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr16,length=90338345,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr17,length=83257441,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr18,length=80373285,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr19,length=58617616,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr20,length=64444167,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr21,length=46709983,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chr22,length=50818468,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chrX,length=156040895,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chrY,length=57227415,assembly="GRCh37",species="Homo sapiens"> | ||
##contig=<ID=chrM,length=16569,assembly="GRCh37",species="Homo sapiens"> | ||
##SAMPLE=<ID=Case_1_father-N1-DNA1-WGS1,Sex="Male",Disease="Unaffected"> | ||
##SAMPLE=<ID=Case_1_index-N1-DNA1-WGS1,Sex="Female",Disease="Affected"> | ||
##SAMPLE=<ID=Case_1_mother-N1-DNA1-WGS1,Sex="Male",Disease="Unaffected"> | ||
##PEDIGREE=<ID=Case_1_father-N1-DNA1-WGS1> | ||
##PEDIGREE=<ID=Case_1_index-N1-DNA1-WGS1,Father="Case_1_father-N1-DNA1-WGS1",Mother="Case_1_mother-N1-DNA1-WGS1"> | ||
##PEDIGREE=<ID=Case_1_mother-N1-DNA1-WGS1> | ||
##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z"> | ||
##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="3.7-0-gcfedb67"> | ||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Case_1_father-N1-DNA1-WGS1 Case_1_index-N1-DNA1-WGS1 Case_1_mother-N1-DNA1-WGS1 | ||
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FAM Case_1_index-N1-DNA1-WGS1 Case_1_father-N1-DNA1-WGS1 Case_1_mother-N1-DNA1-WGS1 2 2 | ||
FAM Case_1_father-N1-DNA1-WGS1 0 0 1 1 | ||
FAM Case_1_mother-N1-DNA1-WGS1 0 0 1 1 |