hammerlab/guacamole — pull request #52 by iskandr (2014-05-07 22:57:44+00:00)
Title: Created simple somatic variant caller

This is a very simple self-contained somatic distributed variant caller. Every ADAMRecord gets pulled apart into an RDD[BaseRead], which are then grouped by their position (and each grouping of BaseReads is a pileup). At each position we then call a variant if there are at least 10 reads of quality >= 20 and the most common normal base is a Match and the most common tumor read is a Mismatch. Obviously, we're not going to win contests on this sort of dumb logic but it's pretty easy to extend.