@gmod/vcf
Version:
High performance streaming Variant Call Format (VCF) parser in pure JavaScript
348 lines • 10.8 kB
JavaScript
"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
exports.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',
},
},
};
//# sourceMappingURL=vcfReserved.js.map