hammerlab/guacamole — pull request #84 by arahuja (2014-05-28 23:05:14+00:00)
Title: Add metrics for variant evaluation

This adds a separate variant evaluation command and the ability to output precision, recall and f1 score on any variant calling run if a truth vcf is available.

This uses the concordance table of ADAM but differs in interpreting its output since we assume that anything that is called (even ref/ref) should be evaluated in case it was a reversion to reference.