@gmod/vcf
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High performance streaming Variant Call Format (VCF) parser in pure JavaScript
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# vcf-js
High performance Variant Call Format (VCF) parser in pure JavaScript.
## Status
[](https://npmjs.org/package/@gmod/vcf)
[](https://codecov.io/gh/GMOD/vcf-js/branch/master)
[](https://github.com/GMOD/vcf-js/actions)
## Usage
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 } 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
## Methods
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()` would be
```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'],
},
SAMPLES: () => ({
HG00096: {
GT: ['0|0'],
AP: ['0.000', '0.000'],
},
}),
GENOTYPES: () => ({
HG00096: '0|0',
}),
}
```
The `variant.SAMPLES()` and `variant.GENOTYPES()` are functions because it does
not try to eagerly parse all the genotype data, so will only do so when you call
either of these which can save time especially if your VCF has a lot of samples
in it.
The `variant.SAMPLES()` function parses out the FORMAT fields, while
`variant.GENOTYPES()` returns just the genotypes string which can be faster if
that is the only information you are interested in
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=<ID=ABC,Number=2,Type=Integer,Description="A description">
```
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 which
case it will be `true`. If no metadata can be found for the entry, it will
assume `Number=1` and `Type=String`.
Some fields are pre-defined by the
[VCF spec](https://samtools.github.io/hts-specs/VCFv4.3.pdf), 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=<ID=ABC,Number=2,Type=Integer,Description="A description">
#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' ]
```
## Breakends
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('C[2:321682[')
// 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
## API
<!-- Generated by documentation.js. Update this documentation by updating the source code. -->
#### Table of Contents
- [VCFParser](#vcfparser)
- [Parameters](#parameters)
- [getMetadata](#getmetadata)
- [Parameters](#parameters-1)
- [parseLine](#parseline)
- [Parameters](#parameters-2)
### VCFParser
Class representing a VCF parser, instantiated with the VCF header.
#### Parameters
- `args`
**[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** 
- `args.header`
**[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**
The VCF header. Supports both LF and CRLF newlines. (optional, default `''`)
- `args.strict`
**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)**
Whether to parse in strict mode or not (default true) (optional, 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=\<ID=DP,...>"
##### Parameters
- `args`
**...[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**
List of metadata filter strings.
Returns **any** An object, string, or number, depending on the filtering
#### parseLine
Parse a VCF line into an object like
```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'],
},
SAMPLES: () => ({
HG00096: {
GT: ['0|0'],
AP: ['0.000', '0.000'],
}
}),
GENOTYPES: () => ({
HG00096: '0|0'
})
}
```
SAMPLES and GENOTYPES methods are functions instead of static data fields
because it avoids parsing the potentially long list of samples from e.g. 1000
genotypes data unless requested.
The SAMPLES function gives all info about the samples
The GENOTYPES function only extracts the raw GT string if it exists, for
potentially optimized parsing by programs that need it
##### Parameters
- `line`
**[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**
A string of a line from a VCF