vip-report-vcf

TypeScript VCF library with support for both reading and writing.

- Supports parsing of nested data such as Ensembl VEP annotations
- Optionally supply a supplementary metadata.json to describe
- Categorical values
- Required values
- Null values

Usage

``ts
import { parseVcf } from "../VcfParser";
import { writeVcf } from "../VcfWriter";

const vcf =
##fileformat=VCFv4.2
##INFO=
##INFO=
##FORMAT=
#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tS0
1\t12\t.\tC\tT\t.\tPASS\tDP=2;H2;\tGT\t0/1
;

const parsedVcf = parseVcf(vcf);

console.log(writeVcf(parsedVcf));
`

Supplementary metadata

Optionally supply a supplementary metadata.json when parsing VCF:

`ts
import { parseVcf } from "../VcfParser";

const metadata: SupplementaryMetadata = {
format: {
IP: {
label: "Inheritance",
description: "Inheritance pattern",
numberType: "OTHER",
separator: ",",
type: "CATEGORICAL",
categories: {
0: { label: "AD", description: "Autosomal dominant" },
1: { label: "AR", description: "Autosomal recessive" },
},
nullValue: { label: "Unknown", description: "Inheritance pattern unknown" },
},
},
info: {
CL: {
label: "Classification",
description: "Variant classification",
numberType: "NUMBER",
numberCount: 1,
type: "CATEGORICAL",
categories: {
B: { label: "Benign" },
LB: { label: "Likely benign" },
VUS: { label: "Variant of uncertain significance" },
LP: { label: "Likely pathogenic" },
P: { label: "Pathogenic" },
},
required: true,
},
},
};

const vcf =
##fileformat=VCFv4.2
##INFO=
##FORMAT=
#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tS0
1\t12\t.\tC\tT\t.\tPASS\tCL=P\tIP\t0
;

const parsedVcf = parseVcf(vcf, metadata);
console.log(parsedVcf.data);
console.log(parsedVcf.metadata);
`

results in

`
[{"c":"1","p":12,"i":[],"r":"C","a":["T"],"q":null,"f":["PASS"],"n":{"CL":"P"},"s":[{"IP":["0"]}]}]

``

Note that currently the metadata is not used in any way when parsing VCF, but only stored in the output container for
usage in downstream tools.