Eric Banks 1ff9463285 Added the RGQ format annotation to monomorphic sites in the VCF output of GenotypeGVCFs. ... Now, instead of stripping out the GQs for mono sites, we transfer them to the RGQ. This is extremely useful for people who want to know how confident the hom ref genotype calls are. Perhaps this is just what CRSP needs for pertinent negatives. Note that I also changed the tool to no longer use the GenotypeSummaries annotation by default since it was adding some seemingly unnecessary annotations (like mean GQ now that we keep the GQ around and number of no-calls). Let me know if this was a mistake (although Laura gave me a thumbs up).		2015-03-13 10:27:20 -04:00
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main	Added the RGQ format annotation to monomorphic sites in the VCF output of GenotypeGVCFs.	2015-03-13 10:27:20 -04:00
test	Merge pull request #807 from broadinstitute/rhl_handle_cigar	2015-02-01 11:09:52 -05:00