MySeq-VCF

myseq-vcf is a browser and node-compatible library for querying Tabix-indexed VCF files by genomic coordinates. Both local and remote files are supported. Queries will only request the necessary blocks of the bgzip-compressed VCF file, enabling efficient targeted analysis of whole-genome-scale VCF files.

myseq-vcf was developed to support MySeq, a web-based personal genome analysis tool designed for educational use. MySeq is described in:

Linderman MD, McElroy L, Chang L. MySeq: privacy-protecting browser-based personal Genome analysis for genomics education and exploration. BMC Med Genomics. 2019 Nov 27;12(1):172.

Usage

The primary entry point is the VCFSource class, which expects a TabixIndexedFile as an argument along with an optional ReferenceGenome object. If a specific reference is not provided, VCFSource will attempt to infer the reference from the "##reference" field in the VCF header or the "##contig" entries in the header. The TabixIndexedFile class expects file readers for the source and index files. Both a LocalFileReader and RemoteFileReader are provided.

For example:

let source = new VCFSource(
  new TabixIndexedFile(
    new RemoteFileReader('http://path/to/vcf.gz'),
    new RemoteFileReader('http://path/to/vcf.gz.tbi'),
  ),
);
source.variants('chr1', 1, 200).then((variants) => {
  variants.forEach(variant => console.log(variant.toString()));
});

VCFSource provides query methods for all variants overlapping a region and for specific variant (position and alleles). That latter supports synthesizing variants with REF/REF genotypes. See the inline documentation for more detail.

Acknowledgements

myseq-vCF incorporates code adapted from JS-Binary-VCF-Tabix and pileup.js.