delangel f8ffda6835 a) Hidden, experimental argument to UnifiedGenotyper that makes code, when in GenotypeGivenAlleles mode, ignore SNP alleles mixed in with indels in complex records - theory is that SNP sites behave statistically differently when doing VQSR so those alleles/sites should be treated separately. ... b) Bug fix: multiallelic indel records where not being treated properly by VQSR because vc.isIndel() returns false with them. Correct general treatment for now is to do (vc.isIndel()||vc.isMixed()). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5973 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-09 19:19:23 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	a) Hidden, experimental argument to UnifiedGenotyper that makes code, when in GenotypeGivenAlleles mode, ignore SNP alleles mixed in with indels in complex records - theory is that SNP sites behave statistically differently when doing VQSR so those alleles/sites should be treated separately.	2011-06-09 19:19:23 +00:00
test	Misc cleanup in VQSR.	2011-06-09 18:37:37 +00:00