bigdatagenomics/adam — pull request #173 by arahuja (2014-03-13 06:08:15+00:00)
Title: Parse annotations out of vcf files

This is a proposal to populate ADAMDatabaseVariantAnnotation by parsing out field in the INFO column of a VCF file. This mostly extends on the existing vcf parsing to ADAMVariant to also parse additional fields and supports integrating new annotations to an existing set.

This adds some preliminary parsing for clinvar, omim, cosmic and dbnsfp

There are still many todos, for example adding more fields to be parsed and populated and generalizing the parsing to allow for anyone to set specific keys that they want to be parsed out, but I wanted to get some discussion around the format and this mega-schema of related variant fields.