High performance streaming Variant Call Format (VCF) parser in pure JavaScript
npm install @gmod/vcfHigh performance Variant Call Format (VCF) parser in pure JavaScript.
This module is best used when combined with some easy way of retrieving the
header and individual lines from a VCF, like the @gmod/tabix module.
``typescript
import { TabixIndexedFile } from '@gmod/tabix'
// with import
import VCF, { parseBreakend, Variant } from '@gmod/vcf'
// with require
const { default: VCF, parseBreakend } = require('@gmod/vcf')
const tbiIndexed = new TabixIndexedFile({ path: '/path/to/my.vcf.gz' })
async function doStuff() {
const headerText = await tbiIndexed.getHeader()
const tbiVCFParser = new VCF({ header: headerText })
const variants = []
await tbiIndexed.getLines('ctgA', 200, 300, line =>
variants.push(tbiVCFParser.parseLine(line)),
)
console.log(variants)
}
`
If you want to stream a VCF file, you can alternatively use something like this
`typescript
const fs = require('fs')
const VCF = require('@gmod/vcf').default
const { createGunzip } = require('zlib')
const readline = require('readline')
const rl = readline.createInterface({
input: fs.createReadStream(process.argv[2]).pipe(createGunzip()),
})
let header = []
let elts = []
let parser = undefined
rl.on('line', function (line) {
if (line.startsWith('#')) {
header.push(line)
return
} else if (!parser) {
parser = new VCF({ header: header.join('\n') })
}
const elt = parser.parseLine(line)
elts.push(elt.INFO.AN[0])
})
rl.on('close', function () {
console.log(elts.reduce((a, b) => a + b, 0) / elts.length)
})
`
This method is used to test @gmod/vcf in https://github.com/brentp/vcf-bench
Given a VCF with a single variant line
`text`
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096
contigA 3000 rs17883296 G T,A 100 PASS NS=3;DP=14;AF=0.5;DB;XYZ=5 GT:AP 0|0:0.000,0.000
The Variant object returned by parseLine() has these properties:
`typescript`
{
CHROM: 'contigA',
POS: 3000,
ID: ['rs17883296'],
REF: 'G',
ALT: ['T', 'A'],
QUAL: 100,
FILTER: 'PASS',
INFO: {
NS: [3],
DP: [14],
AF: [0.5],
DB: true,
XYZ: ['5'],
},
}
The Variant class also has methods for accessing sample data:
- variant.SAMPLES() - returns full sample data with all FORMAT fields parsedvariant.GENOTYPES()
- - returns just the GT strings (faster if that's all youvariant.processGenotypes(callback)
need)
- - calls a callback for each genotype
without allocating strings (fastest for counting/iteration)
These methods lazily parse the genotype data, so they only do work when called.
This saves time especially if your VCF has many samples (e.g. 1000 Genomes).
The parser will try to convert the values in INFO and FORMAT to the proper types
using the header metadata. For example, if there is a header line like
`text`
##INFO=
The parser will expect any INFO entry ABC to be an array of two integers, so it
would convert ABC=12,20 to { ABC: [12, 20] }.
Each INFO entry value will be an array unless Type=Flag is specified, in whichtrue
case it will be . If no metadata can be found for the entry, it willNumber=1
assume and Type=String.
Some fields are pre-defined by the
VCF spec, which is why in
the variant object above "DP" was parsed as an integer (it is defined in the VCF
spec), but "XYZ" was left as a string (it is not defined in either the VCF spec
or the header).
Metadata can be accessed with the getMetadata() method, including all the
built-in metadata from the VCF spec. With no parameters it will return all the
data. Any parameters passed will further filter the metadata. For example, for a
VCF with this header:
`text`
##INFO=
#CHROM POS ID REF ALT QUAL FILTER INFO
you can access the VCF's header metadata like (some output omitted for clarity):
`typescript
> console.log(vcfParser.getMetadata())
{ INFO:
{ AA:
{ Number: 1, Type: 'String', Description: 'Ancestral Allele' },
...
ABC: { Number: 2, Type: 'Integer', Description: 'A description' } },
FORMAT:
{ AD:
{ Number: 'R',
Type: 'Integer',
Description: 'Read depth for each allele' },
...
ALT:
{ DEL: { Description: 'Deletion relative to the reference' },
...
FILTER: { PASS: { Description: 'Passed all filters' } } }
> console.log(vcfParser.getMetadata('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' },
...
ABC: { Number: 2, Type: 'Integer', Description: 'A description' } }
> console.log(vcfParser.getMetadata('INFO', 'DP'))
{ Number: 1, Type: 'Integer', Description: 'Total Depth' }
> console.log(vcfParser.getMetadata('INFO', 'DP', 'Number'))
1
`
A list of sample names is also available in the samples attribute of the
parser object:
`typescript`
> console.log(vcfParser.samples)
[ 'HG00096' ]
We offer a helper function to parse breakend strings. We used to parse these
automatically but it is now a helper function
`js
import { parseBreakend } from '@gmod/vcf'
parseBreakend('C2:321682[')
// output
//
// {
// "MateDirection": "right",
// "Replacement": "C",
// "MatePosition": "2:321682",
// "Join": "right"
// }
`
- The C\[2:321682\[ parses as "Join": "right" because the BND is after the C
base
- The C\[2:321682\[ also is given "MateDirection": "right" because the square
brackets point to the right.
- The spec never has the square brackets pointing in different directions.
Instead, the different types of joins can be imagined as follows
For the above vcf line where chr13:123456->C\[2:321682\[ then we have this
chr13:123456
-------------C\
\
\
\
\
\
\
\
\--------------
chr2:321682
If the alt was instead chr13:123456->\[2:321682\[C then the the "Join" would be
"left" since the "BND" is before "C" and then the breakend structure looks like
this
chr13:123456
|C--------------------
|
|
|
|
|
|
|
|
|
|
----------------------
chr2:321682
#### Table of Contents
- [VCFParser
- Parameters
- getMetadata
- parseLine
- Variant
- SAMPLES
- GENOTYPES
- processGenotypes
Class representing a VCF parser, instantiated with the VCF header.
#### Parameters
- args.header string - The VCF header. Supports both LF and CRLF newlines.args.strict
- boolean - Whether to parse in strict mode or not (default
true)
#### getMetadata
Get metadata filtered by the elements in args. For example, can pass ('INFO',
'DP') to only get info on an metadata tag that was like "##INFO=\
##### Parameters
- ...args string[] - List of metadata filter strings.
Returns any An object, string, or number, depending on the filtering
#### parseLine
Parse a VCF line into a Variant object.
##### Parameters
- line string - A string of a line from a VCF
Returns Variant A Variant instance with the parsed data
Class representing a parsed VCF variant line. Has data properties (CHROM, POS,
ID, REF, ALT, QUAL, FILTER, INFO, FORMAT) and methods for accessing sample data.
#### SAMPLES
Returns full sample data with all FORMAT fields parsed.
Returns **Record\
#### GENOTYPES
Returns just the GT strings for each sample (faster than SAMPLES if you only
need genotypes).
Returns Record\
#### processGenotypes
Calls a callback for each genotype without allocating strings. Useful for
counting or iterating over genotypes with minimal memory allocation.
##### Parameters
- callback (str: string, start: number, end: number) => any - Called forstr.slice(start, end)
each genotype with the raw string and indices. Use tostr.charCodeAt(start)` to read characters
extract the genotype string, or
without allocation.