ga4gh/server — pull request #9 by jeromekelleher (2014-09-02 14:36:05+00:00)
Title: Wormtable backend to serve variants from VCF

This pull request is a proposal for a backend to serve variant data based on VCF files. The backend uses VCF data converted into [wormtable](https://pypi.python.org/pypi/wormtable) format using the `vcf2wt` utility distributed with wormtable. Scalability in terms of data set size is quite good, and it has been tested over the full [2011](http://goo.gl/LFbQHt) and [2013](http://goo.gl/YxaxCq) 1000 Genomes datasets.

The backend currently supports the `variants/search` method using coordinates (`start` and `end`) and names (`variantName`). The `CHROM` column in VCF is mapped to the `referenceName` and is fully supported. Multiple variant sets are also supported (although querying over multiple variant sets at the same time currently does not work). We can also specify the `callSetIds` we wish to have returned, and these are currently directly mapped to the sample name in VCF.

See the README for installation instructions and for the location of example data.