@gmod/vcf

vcf-js

VCF (variant call format) parser

Usage

import { TabixIndexedFile } from '@gmod/tabix'
import VCF from '@gmod/vcf'

const tbiIndexed = new TabixIndexedFile({ path: '/path/to/my.vcf.gz' })

const headerText = await tbiIndexed.getHeader()
const parser = new VCF({ header: headerText }) // strict?: boolean (default true)

const variants = []
await tbiIndexed.getLines('ctgA', 200, 300, line =>
  variants.push(parser.parseLine(line)),
)

Variant

parseLine(line) returns a Variant with these fields:

{
  CHROM: 'contigA',
  POS: 3000,
  ID: ['rs17883296'],
  REF: 'G',
  ALT: ['T', 'A'],
  QUAL: 100,
  FILTER: 'PASS', // 'PASS' | string[] of filter names | undefined if '.'
  INFO: {
    NS: [3],
    DP: [14],
    AF: [0.5],
    DB: true,   // Flag type
    XYZ: ['5'], // unknown fields default to Number=1, Type=String
  },
}

INFO and FORMAT values are typed using header metadata. Values are arrays unless Type=Flag, in which case they are true. Fields defined in the VCF spec are typed even without a header entry.

Sample methods

• variant.SAMPLES() — full sample data with all FORMAT fields parsed
• variant.GENOTYPES() — GT strings only (faster)
• variant.processGenotypes(callback) — iterate genotypes without allocating strings (fastest)

let homRef = 0
variant.processGenotypes((str, start, end) => {
  if (
    end - start === 3 && // e.g. "0|0"
    str.charCodeAt(start) === 48 && // 48 = '0'
    str.charCodeAt(start + 2) === 48
  ) {
    homRef++
  }
})

Sample data is lazily parsed — nothing is computed until these methods are called.

Metadata

parser.getMetadata(...keys) returns header metadata, filtered by the keys provided:

parser.getMetadata('INFO', 'DP')
// { Number: 1, Type: 'Integer', Description: 'Total Depth' }

parser.getMetadata('INFO', 'DP', 'Number')
// 1

Call with no arguments to get all metadata. parser.samples lists sample names.

Streaming

To parse a plain VCF without tabix, collect header lines until the first non-header line, then construct the parser:

import fs from 'fs'
import VCF from '@gmod/vcf'
import { createGunzip } from 'zlib'
import readline from 'readline'

const rl = readline.createInterface({
  input: fs.createReadStream('file.vcf.gz').pipe(createGunzip()),
})

const header = []
let parser

rl.on('line', line => {
  if (line.startsWith('#')) {
    header.push(line)
  } else {
    if (!parser) {
      parser = new VCF({ header: header.join('\n') })
    }
    const variant = parser.parseLine(line)
    console.log(variant.CHROM, variant.POS)
  }
})

Breakends

parseBreakend(alt) parses a breakend ALT string:

import { parseBreakend } from '@gmod/vcf'

parseBreakend('C[2:321682[')
// { MateDirection: 'right', Replacement: 'C', MatePosition: '2:321682', Join: 'right' }

All four bracket forms from the VCF spec:

ALT form	Join	MateDirection
t[p[	right	right
t]p]	right	left
[p[t	left	right
]p]t	left	left

• Join — whether the replacement base appears before (right) or after (left) the mate position
• MateDirection — [ means the mate sequence extends rightward; ] means leftward

Single breakends

When the ALT starts or ends with ., parseBreakend returns SingleBreakend: true with no MatePosition:

parseBreakend('C.')
// { Join: 'right', Replacement: 'C', SingleBreakend: true }

parseBreakend('.ACGT')
// { Join: 'left', Replacement: 'ACGT', SingleBreakend: true }

Publishing

Trusted publishing via GitHub Actions.

npm version patch  # or minor/major