@gmod/vcf

export default { // INFO fields InfoFields: { // from the VCF4.3 spec, https://samtools.github.io/hts-specs/VCFv4.3.pdf 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', }, // specifically for structural variants IMPRECISE: { Number: 0, Type: 'Flag', Description: 'Imprecise structural variation', }, NOVEL: { Number: 0, Type: 'Flag', Description: 'Indicates a novel structural variation', }, // For precise variants, END is POS + length of REF allele - 1, // and the for imprecise variants the corresponding best estimate. SVTYPE: { Number: 1, Type: 'String', Description: 'Type of structural variant', }, // Value should be one of DEL, INS, DUP, INV, CNV, BND. This key can // be derived from the REF/ALT fields but is useful for filtering. SVLEN: { Number: null, Type: 'Integer', Description: 'Difference in length between REF and ALT alleles', }, // One value for each ALT allele. Longer ALT alleles (e.g. insertions) // have positive values, shorter ALT alleles (e.g. deletions) // have negative values. 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', }, // For precise variants, the consensus sequence the alternate allele assembly // is derivable from the REF and ALT fields. However, the alternate allele // assembly file may contain additional information about the characteristics // of the alt allele contigs. 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 fields GenotypeFields: { // from the VCF4.3 spec, https://samtools.github.io/hts-specs/VCFv4.3.pdf 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 fields AltTypes: { 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 fields FilterTypes: { PASS: { Description: 'Passed all filters', }, }, }