Tool: VCFStream.js - Stream and filter a VCF file in Node/JavaScript
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gravatar for Dan D
5 months ago by
Dan D6.4k
Tennessee
Dan D6.4k wrote:

https://github.com/DeeSeeDee/vcf-stream

VCFStream.js

I built this to get more familiar with ES2015 syntax and work through the finer points of the VCF specification. Hopefully it's useful or has the potential to become useful to others in the bioinformatics field.

There are two main classes in the package: VCFStream and Variant. An instance of the Variant class is intended to encapsulate a single variant from a VCF file.

VCFStream is what reads in a single VCF file containing one or more samples. It automatically reads the VCF header via a Node stream and builds its internal data structures based on the information in the header. After the instance ingests the header, it emits a header event and pauses the stream.

At this point filters can be added to the stream. Users can filter on specific samples by passing an array of sample names to the addSampleFilter method. Regions, denoted by a contig (chromosome) name, start position, and an optional end position, can be added using the addInterval method.

Other filters include:

  • addInfoFlagFilter to filter on the presence or absence of an INFO field having a "Flag" type.
  • addStringFilter to filter in an exact or loose-match fashion on INFO or FORMAT fields having a String type.
  • addRangeFilter to filter on numeric INFO or FORMAT fields using lower and optional upper numeric bounds

The latter two filters take a matchType property in the filter object. This can be one of three values:

  • all All items in the field for the variant must meet the filtering criteria
  • any At least one item must meet the filtering criteria
  • none No item in the field may meet the filtering criteria.

You can add your own filtering function as well. For example, if you to add a filter that only passes variants which are single-nucleotide polymorphisms:

vcfStream.filters.push((variant) => { return variant.isSNP; });

Any variant that passes all of the filters in place will be stored. When that variant is processed, the VCFStream instance will emit a variant event.

When the VCFStream instance reaches the end of the file, it will emit an end event.

It's backed by a large suite of unit tests. All suggestions welcome. If others find this interesting or worthwhile, I will invest more time to create full documentation, and add many more features. Please post a comment here or on the Github project with your feedback. All collaborations and pull requests are welcome too, of course. Thanks!

javascript tool nodejs vcf • 353 views
ADD COMMENTlink written 5 months ago by Dan D6.4k
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