vcf-js
vcf-js copied to clipboard
Published
20 hours ago •
GMOD
GMOD
Some VCF metadata headers are parsed with keys named undefined (e.g. PEDIGREE, ID)
Examples
volvox 1000g example, with PEDIGREE
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##source=BCM:SNPTools:hapfuse
##reference=volvox_example
##ALT=<ID=TEST:TESTSUB,Description="User-defined symbolic ALT test with subtype">
##contig=<ID=ctgA,URL=ftp://somewhere.org/assembly.fa,http://example.com/contigs/ctgA>
##SAMPLE=<ID=Blood,Genomes=Germline,Mixture=1.,Description="Patient germline genome">
##SAMPLE=<ID=TissueSample,Genomes=Germline;Tumor,Mixture=.3;.7,Description="Patient germline genome;Patient tumor genome">
##PEDIGREE=<Derived=PRIMARY-TUMOR-GENOME-ID,Original=GERMLINE-GENOME-ID>
##PEDIGREE=<Derived=SECONDARY1-TUMOR-GENOME-ID,Original=PRIMARY-TUMOR-GENOME-ID>
##PEDIGREE=<Derived=SECONDARY2-TUMOR-GENOME-ID,Original=PRIMARY-TUMOR-GENOME-ID>
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=AP,Number=2,Type=Float,Description="Allelic Probability, P(Allele=1|Haplotype)">
{
"INFO": {
"AA": {
"Number": 1,
"Type": "String",
"Description": "Ancestral Allele"
},
"AC": {
"Number": "A",
"Type": "Integer",
"Description": "Allele count in genotypes, for each ALT allele, in the same order as listed"
},
"AD": {
"Number": "R",
"Type": "Integer",
"Description": "Total read depth for each allele"
},
"ADF": {
"Number": "R",
"Type": "Integer",
"Description": "Read depth for each allele on the forward strand"
},
"ADR": {
"Number": "R",
"Type": "Integer",
"Description": "Read depth for each allele on the reverse strand"
},
"AF": {
"Number": "A",
"Type": "Float",
"Description": "Allele Frequency"
},
"AN": {
"Number": 1,
"Type": "Integer",
"Description": "Total number of alleles in called genotypes"
},
"BQ": {
"Number": 1,
"Type": "Float",
"Description": "RMS base quality"
},
"CIGAR": {
"Number": 1,
"Type": "Float",
"Description": "Cigar string describing how to align an alternate allele to the reference allele"
},
"DB": {
"Number": 0,
"Type": "Flag",
"Description": "dbSNP membership, build 129"
},
"DP": {
"Number": 1,
"Type": "Integer",
"Description": "Total Depth"
},
"END": {
"Number": 1,
"Type": "Integer",
"Description": "End position (for use with symbolic alleles)"
},
"H2": {
"Number": 0,
"Type": "Flag",
"Description": "HapMap2 membership"
},
"H3": {
"Number": 0,
"Type": "Flag",
"Description": "HapMap3 membership"
},
"MQ": {
"Number": 1,
"Type": null,
"Description": "RMS mapping quality"
},
"MQ0": {
"Number": 1,
"Type": "Integer",
"Description": "Number of MAPQ == 0 reads"
},
"NS": {
"Number": 1,
"Type": "Integer",
"Description": "Number of Samples With Data"
},
"SB": {
"Number": 4,
"Type": "Integer",
"Description": "Strand bias"
},
"SOMATIC": {
"Number": 0,
"Type": "Flag",
"Description": "Somatic mutation (for cancer genomics)"
},
"VALIDATED": {
"Number": 0,
"Type": "Flag",
"Description": "Validated by follow-up experiment"
},
"1000G": {
"Number": 0,
"Type": "Flag",
"Description": "1000 Genomes membership"
},
"IMPRECISE": {
"Number": 0,
"Type": "Flag",
"Description": "Imprecise structural variation"
},
"NOVEL": {
"Number": 0,
"Type": "Flag",
"Description": "Indicates a novel structural variation"
},
"SVTYPE": {
"Number": 1,
"Type": "String",
"Description": "Type of structural variant"
},
"SVLEN": {
"Number": null,
"Type": "Integer",
"Description": "Difference in length between REF and ALT alleles"
},
"CIPOS": {
"Number": 2,
"Type": "Integer",
"Description": "Confidence interval around POS for imprecise variants"
},
"CIEND": {
"Number": 2,
"Type": "Integer",
"Description": "Confidence interval around END for imprecise variants"
},
"HOMLEN": {
"Type": "Integer",
"Description": "Length of base pair identical micro-homology at event breakpoints"
},
"HOMSEQ": {
"Type": "String",
"Description": "Sequence of base pair identical micro-homology at event breakpoints"
},
"BKPTID": {
"Type": "String",
"Description": "ID of the assembled alternate allele in the assembly file"
},
"MEINFO": {
"Number": 4,
"Type": "String",
"Description": "Mobile element info of the form NAME,START,END,POLARITY"
},
"METRANS": {
"Number": 4,
"Type": "String",
"Description": "Mobile element transduction info of the form CHR,START,END,POLARITY"
},
"DGVID": {
"Number": 1,
"Type": "String",
"Description": "ID of this element in Database of Genomic Variation"
},
"DBVARID": {
"Number": 1,
"Type": "String",
"Description": "ID of this element in DBVAR"
},
"DBRIPID": {
"Number": 1,
"Type": "String",
"Description": "ID of this element in DBRIP"
},
"MATEID": {
"Number": null,
"Type": "String",
"Description": "ID of mate breakends"
},
"PARID": {
"Number": 1,
"Type": "String",
"Description": "ID of partner breakend"
},
"EVENT": {
"Number": 1,
"Type": "String",
"Description": "ID of event associated to breakend"
},
"CILEN": {
"Number": 2,
"Type": "Integer",
"Description": "Confidence interval around the inserted material between breakend"
},
"DPADJ": {
"Type": "Integer",
"Description": "Read Depth of adjacency"
},
"CN": {
"Number": 1,
"Type": "Integer",
"Description": "Copy number of segment containing breakend"
},
"CNADJ": {
"Number": null,
"Type": "Integer",
"Description": "Copy number of adjacency"
},
"CICN": {
"Number": 2,
"Type": "Integer",
"Description": "Confidence interval around copy number for the segment"
},
"CICNADJ": {
"Number": null,
"Type": "Integer",
"Description": "Confidence interval around copy number for the adjacency"
}
},
"FORMAT": {
"AD": {
"Number": "R",
"Type": "Integer",
"Description": "Read depth for each allele"
},
"ADF": {
"Number": "R",
"Type": "Integer",
"Description": "Read depth for each allele on the forward strand"
},
"ADR": {
"Number": "R",
"Type": "Integer",
"Description": "Read depth for each allele on the reverse strand"
},
"DP": {
"Number": 1,
"Type": "Integer",
"Description": "Read depth"
},
"EC": {
"Number": "A",
"Type": "Integer",
"Description": "Expected alternate allele counts"
},
"FT": {
"Number": 1,
"Type": "String",
"Description": "Filter indicating if this genotype was \"called\""
},
"GL": {
"Number": "G",
"Type": "Float",
"Description": "Genotype likelihoods"
},
"GP": {
"Number": "G",
"Type": "Float",
"Description": "Genotype posterior probabilities"
},
"GQ": {
"Number": 1,
"Type": "Integer",
"Description": "Conditional genotype quality"
},
"GT": {
"Number": 1,
"Type": "String",
"Description": "Genotype"
},
"HQ": {
"Number": 2,
"Type": "Integer",
"Description": "Haplotype quality"
},
"MQ": {
"Number": 1,
"Type": "Integer",
"Description": "RMS mapping quality"
},
"PL": {
"Number": "G",
"Type": "Integer",
"Description": "Phred-scaled genotype likelihoods rounded to the closest integer"
},
"PQ": {
"Number": 1,
"Type": "Integer",
"Description": "Phasing quality"
},
"PS": {
"Number": 1,
"Type": "Integer",
"Description": "Phase set"
},
"AP": {
"Number": 2,
"Type": "Float",
"Description": "Allelic Probability, P(Allele=1|Haplotype)"
}
},
"ALT": {
"DEL": {
"Description": "Deletion relative to the reference"
},
"INS": {
"Description": "Insertion of novel sequence relative to the reference"
},
"DUP": {
"Description": "Region of elevated copy number relative to the reference"
},
"INV": {
"Description": "Inversion of reference sequence"
},
"CNV": {
"Description": "Copy number variable region (may be both deletion and duplication)"
},
"DUP:TANDEM": {
"Description": "Tandem duplication"
},
"DEL:ME": {
"Description": "Deletion of mobile element relative to the reference"
},
"INS:ME": {
"Description": "Insertion of a mobile element relative to the reference"
},
"NON_REF": {
"Description": "Represents any possible alternative allele at this location"
},
"*": {
"Description": "Represents any possible alternative allele at this location"
},
"TEST:TESTSUB": {
"Description": "User-defined symbolic ALT test with subtype"
}
},
"FILTER": {
"PASS": {
"Description": "Passed all filters"
},
"q10": {
"Description": "Quality below 10"
},
"s50": {
"Description": "Less than 50% of samples have data"
}
},
"fileformat": "VCFv4.1",
"fileDate": "20090805",
"source": "BCM:SNPTools:hapfuse",
"reference": "volvox_example",
"contig": {
"20": {
"length": "62435964",
"assembly": "B36",
"md5": "f126cdf8a6e0c7f379d618ff66beb2da",
"species": "Homo sapiens",
"taxonomy": "x"
},
"ctgA": {
"URL": "ftp://somewhere.org/assembly.fa",
"http://example.com/contigs/ctgA": null
}
},
"phasing": "partial",
"SAMPLE": {
"Blood": {
"Genomes": "Germline",
"Mixture": "1.",
"Description": "Patient germline genome"
},
"TissueSample": {
"Genomes": "Germline;Tumor",
"Mixture": ".3;.7",
"Description": "Patient germline genome;Patient tumor genome"
}
},
"PEDIGREE": {
"undefined": {
"Derived": "SECONDARY2-TUMOR-GENOME-ID",
"Original": "PRIMARY-TUMOR-GENOME-ID"
}
}
}
ID example from https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar.vcf.gz
##fileformat=VCFv4.1
##fileDate=2023-02-13
##source=ClinVar
##reference=GRCh37
##ID=<Description="ClinVar Variation ID">
##INFO=<ID=AF_ESP,Number=1,Type=Float,Description="allele frequencies from GO-ESP">
##INFO=<ID=AF_EXAC,Number=1,Type=Float,Description="allele frequencies from ExAC">
##INFO=<ID=AF_TGP,Number=1,Type=Float,Description="allele frequencies from TGP">
##INFO=<ID=ALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB">
##INFO=<ID=CLNDNINCL,Number=.,Type=String,Description="For included Variant : ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN">
##INFO=<ID=CLNDISDBINCL,Number=.,Type=String,Description="For included Variant: Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.">
##INFO=<ID=CLNREVSTAT,Number=.,Type=String,Description="ClinVar review status for the Variation ID">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant; multiple values are separated by a vertical bar">
##INFO=<ID=CLNSIGCONF,Number=.,Type=String,Description="Conflicting clinical significance for this single variant; multiple values are separated by a vertical bar">
##INFO=<ID=CLNSIGINCL,Number=.,Type=String,Description="Clinical significance for a haplotype or genotype that includes this variant. Reported as pairs of VariationID:clinical significance; multiple values are separated by a vertical bar">
##INFO=<ID=CLNVC,Number=1,Type=String,Description="Variant type">
##INFO=<ID=CLNVCSO,Number=1,Type=String,Description="Sequence Ontology id for variant type">
##INFO=<ID=CLNVI,Number=.,Type=String,Description="the variant's clinical sources reported as tag-value pairs of database and variant identifier">
##INFO=<ID=DBVARID,Number=.,Type=String,Description="nsv accessions from dbVar for the variant">
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Gene(s) for the variant reported as gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|)">
##INFO=<ID=MC,Number=.,Type=String,Description="comma separated list of molecular consequence in the form of Sequence Ontology ID|molecular_consequence">
##INFO=<ID=ORIGIN,Number=.,Type=String,Description="Allele origin. One or more of the following values may be added: 0 - unknown; 1 - germline; 2 - somatic; 4 - inherited; 8 - paternal; 16 - maternal; 32 - de-novo; 64 - biparental; 128 - uniparental; 256 - not-tested; 512 - tested-inconclusive; 1073741824 - other">
##INFO=<ID=RS,Number=.,Type=String,Description="dbSNP ID (i.e. rs number)">
##INFO=<ID=SSR,Number=1,Type=Integer,Description="Variant Suspect Reason Codes. One or more of the following values may be added: 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other">
{
"INFO": {
"AA": {
"Number": 1,
"Type": "String",
"Description": "Ancestral allele"
},
"AC": {
"Number": "A",
"Type": "Integer",
"Description": "Allele count in genotypes, for each ALT allele, in the same order as listed"
},
"AD": {
"Number": "R",
"Type": "Integer",
"Description": "Total read depth for each allele"
},
"ADF": {
"Number": "R",
"Type": "Integer",
"Description": "Read depth for each allele on the forward strand"
},
"ADR": {
"Number": "R",
"Type": "Integer",
"Description": "Read depth for each allele on the reverse strand"
},
"AF": {
"Number": "A",
"Type": "Float",
"Description": "Allele frequency for each ALT allele in the same order as listed (estimated from primary data, not called genotypes)"
},
"AN": {
"Number": 1,
"Type": "Integer",
"Description": "Total number of alleles in called genotypes"
},
"BQ": {
"Number": 1,
"Type": "Float",
"Description": "RMS base quality"
},
"CIGAR": {
"Number": 1,
"Type": "Float",
"Description": "Cigar string describing how to align an alternate allele to the reference allele"
},
"DB": {
"Number": 0,
"Type": "Flag",
"Description": "dbSNP membership"
},
"DP": {
"Number": 1,
"Type": "Integer",
"Description": "combined depth across samples"
},
"END": {
"Number": 1,
"Type": "Integer",
"Description": "End position (for use with symbolic alleles)"
},
"H2": {
"Number": 0,
"Type": "Flag",
"Description": "HapMap2 membership"
},
"H3": {
"Number": 0,
"Type": "Flag",
"Description": "HapMap3 membership"
},
"MQ": {
"Number": 1,
"Type": null,
"Description": "RMS mapping quality"
},
"MQ0": {
"Number": 1,
"Type": "Integer",
"Description": "Number of MAPQ == 0 reads"
},
"NS": {
"Number": 1,
"Type": "Integer",
"Description": "Number of samples with data"
},
"SB": {
"Number": 4,
"Type": "Integer",
"Description": "Strand bias"
},
"SOMATIC": {
"Number": 0,
"Type": "Flag",
"Description": "Somatic mutation (for cancer genomics)"
},
"VALIDATED": {
"Number": 0,
"Type": "Flag",
"Description": "Validated by follow-up experiment"
},
"1000G": {
"Number": 0,
"Type": "Flag",
"Description": "1000 Genomes membership"
},
"IMPRECISE": {
"Number": 0,
"Type": "Flag",
"Description": "Imprecise structural variation"
},
"NOVEL": {
"Number": 0,
"Type": "Flag",
"Description": "Indicates a novel structural variation"
},
"SVTYPE": {
"Number": 1,
"Type": "String",
"Description": "Type of structural variant"
},
"SVLEN": {
"Number": null,
"Type": "Integer",
"Description": "Difference in length between REF and ALT alleles"
},
"CIPOS": {
"Number": 2,
"Type": "Integer",
"Description": "Confidence interval around POS for imprecise variants"
},
"CIEND": {
"Number": 2,
"Type": "Integer",
"Description": "Confidence interval around END for imprecise variants"
},
"HOMLEN": {
"Type": "Integer",
"Description": "Length of base pair identical micro-homology at event breakpoints"
},
"HOMSEQ": {
"Type": "String",
"Description": "Sequence of base pair identical micro-homology at event breakpoints"
},
"BKPTID": {
"Type": "String",
"Description": "ID of the assembled alternate allele in the assembly file"
},
"MEINFO": {
"Number": 4,
"Type": "String",
"Description": "Mobile element info of the form NAME,START,END,POLARITY"
},
"METRANS": {
"Number": 4,
"Type": "String",
"Description": "Mobile element transduction info of the form CHR,START,END,POLARITY"
},
"DGVID": {
"Number": 1,
"Type": "String",
"Description": "ID of this element in Database of Genomic Variation"
},
"DBVARID": {
"Number": ".",
"Type": "String",
"Description": "nsv accessions from dbVar for the variant"
},
"DBRIPID": {
"Number": 1,
"Type": "String",
"Description": "ID of this element in DBRIP"
},
"MATEID": {
"Number": null,
"Type": "String",
"Description": "ID of mate breakends"
},
"PARID": {
"Number": 1,
"Type": "String",
"Description": "ID of partner breakend"
},
"EVENT": {
"Number": 1,
"Type": "String",
"Description": "ID of event associated to breakend"
},
"CILEN": {
"Number": 2,
"Type": "Integer",
"Description": "Confidence interval around the inserted material between breakend"
},
"DPADJ": {
"Type": "Integer",
"Description": "Read Depth of adjacency"
},
"CN": {
"Number": 1,
"Type": "Integer",
"Description": "Copy number of segment containing breakend"
},
"CNADJ": {
"Number": null,
"Type": "Integer",
"Description": "Copy number of adjacency"
},
"CICN": {
"Number": 2,
"Type": "Integer",
"Description": "Confidence interval around copy number for the segment"
},
"CICNADJ": {
"Number": null,
"Type": "Integer",
"Description": "Confidence interval around copy number for the adjacency"
},
"AF_ESP": {
"Number": 1,
"Type": "Float",
"Description": "allele frequencies from GO-ESP"
},
"AF_EXAC": {
"Number": 1,
"Type": "Float",
"Description": "allele frequencies from ExAC"
},
"AF_TGP": {
"Number": 1,
"Type": "Float",
"Description": "allele frequencies from TGP"
},
"ALLELEID": {
"Number": 1,
"Type": "Integer",
"Description": "the ClinVar Allele ID"
},
"CLNDN": {
"Number": ".",
"Type": "String",
"Description": "ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB"
},
"CLNDNINCL": {
"Number": ".",
"Type": "String",
"Description": "For included Variant : ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB"
},
"CLNDISDB": {
"Number": ".",
"Type": "String",
"Description": "Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN"
},
"CLNDISDBINCL": {
"Number": ".",
"Type": "String",
"Description": "For included Variant: Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN"
},
"CLNHGVS": {
"Number": ".",
"Type": "String",
"Description": "Top-level (primary assembly, alt, or patch) HGVS expression."
},
"CLNREVSTAT": {
"Number": ".",
"Type": "String",
"Description": "ClinVar review status for the Variation ID"
},
"CLNSIG": {
"Number": ".",
"Type": "String",
"Description": "Clinical significance for this single variant; multiple values are separated by a vertical bar"
},
"CLNSIGCONF": {
"Number": ".",
"Type": "String",
"Description": "Conflicting clinical significance for this single variant; multiple values are separated by a vertical bar"
},
"CLNSIGINCL": {
"Number": ".",
"Type": "String",
"Description": "Clinical significance for a haplotype or genotype that includes this variant. Reported as pairs of VariationID:clinical significance; multiple values are separated by a vertical bar"
},
"CLNVC": {
"Number": 1,
"Type": "String",
"Description": "Variant type"
},
"CLNVCSO": {
"Number": 1,
"Type": "String",
"Description": "Sequence Ontology id for variant type"
},
"CLNVI": {
"Number": ".",
"Type": "String",
"Description": "the variant's clinical sources reported as tag-value pairs of database and variant identifier"
},
"GENEINFO": {
"Number": 1,
"Type": "String",
"Description": "Gene(s) for the variant reported as gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|)"
},
"MC": {
"Number": ".",
"Type": "String",
"Description": "comma separated list of molecular consequence in the form of Sequence Ontology ID|molecular_consequence"
},
"ORIGIN": {
"Number": ".",
"Type": "String",
"Description": "Allele origin. One or more of the following values may be added: 0 - unknown; 1 - germline; 2 - somatic; 4 - inherited; 8 - paternal; 16 - maternal; 32 - de-novo; 64 - biparental; 128 - uniparental; 256 - not-tested; 512 - tested-inconclusive; 1073741824 - other"
},
"RS": {
"Number": ".",
"Type": "String",
"Description": "dbSNP ID (i.e. rs number)"
},
"SSR": {
"Number": 1,
"Type": "Integer",
"Description": "Variant Suspect Reason Codes. One or more of the following values may be added: 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other"
}
},
"FORMAT": {
"AD": {
"Number": "R",
"Type": "Integer",
"Description": "Read depth for each allele"
},
"ADF": {
"Number": "R",
"Type": "Integer",
"Description": "Read depth for each allele on the forward strand"
},
"ADR": {
"Number": "R",
"Type": "Integer",
"Description": "Read depth for each allele on the reverse strand"
},
"DP": {
"Number": 1,
"Type": "Integer",
"Description": "Read depth"
},
"EC": {
"Number": "A",
"Type": "Integer",
"Description": "Expected alternate allele counts"
},
"FT": {
"Number": 1,
"Type": "String",
"Description": "Filter indicating if this genotype was \"called\""
},
"GL": {
"Number": "G",
"Type": "Float",
"Description": "Genotype likelihoods"
},
"GP": {
"Number": "G",
"Type": "Float",
"Description": "Genotype posterior probabilities"
},
"GQ": {
"Number": 1,
"Type": "Integer",
"Description": "Conditional genotype quality"
},
"GT": {
"Number": 1,
"Type": "String",
"Description": "Genotype"
},
"HQ": {
"Number": 2,
"Type": "Integer",
"Description": "Haplotype quality"
},
"MQ": {
"Number": 1,
"Type": "Integer",
"Description": "RMS mapping quality"
},
"PL": {
"Number": "G",
"Type": "Integer",
"Description": "Phred-scaled genotype likelihoods rounded to the closest integer"
},
"PQ": {
"Number": 1,
"Type": "Integer",
"Description": "Phasing quality"
},
"PS": {
"Number": 1,
"Type": "Integer",
"Description": "Phase set"
}
},
"ALT": {
"DEL": {
"Description": "Deletion relative to the reference"
},
"INS": {
"Description": "Insertion of novel sequence relative to the reference"
},
"DUP": {
"Description": "Region of elevated copy number relative to the reference"
},
"INV": {
"Description": "Inversion of reference sequence"
},
"CNV": {
"Description": "Copy number variable region (may be both deletion and duplication)"
},
"DUP:TANDEM": {
"Description": "Tandem duplication"
},
"DEL:ME": {
"Description": "Deletion of mobile element relative to the reference"
},
"INS:ME": {
"Description": "Insertion of a mobile element relative to the reference"
},
"NON_REF": {
"Description": "Represents any possible alternative allele at this location"
},
"*": {
"Description": "Represents any possible alternative allele at this location"
}
},
"FILTER": {
"PASS": {
"Description": "Passed all filters"
}
},
"fileformat": "VCFv4.1",
"fileDate": "2023-02-13",
"source": "ClinVar",
"reference": "GRCh37",
"ID": {
"undefined": {
"Description": "ClinVar Variation ID"
}
}
}
