gatk-3.8

Author	SHA1	Message	Date
depristo	d316cbad4c	VariantFilteration now accepts a VCF rod in addition to an input geli. It will then annotate this VCF file with filtering information in the INFO field too. --OnlyAnnotate will not write in filtering output git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2008 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-10 13:24:58 +00:00
aaron	0cc634ed5d	-Renamed rodVariants to RodGeliText -Remove KGenomesSNPROD -Remove rodFLT -Renamed rodGFF to RodGenotypeChipAsGFF -Fixed a problem in SSGenotypeCall -Added basic SSGenotype Test class -Make VCFHeader constructors public git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1536 348d0f76-0448-11de-a6fe-93d51630548a	2009-09-04 18:40:43 +00:00
ebanks	1a299dd459	Require each filter or feature to declare whether or not they want mapping quality zero reads in the alignment context git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1486 348d0f76-0448-11de-a6fe-93d51630548a	2009-08-31 03:31:37 +00:00
ebanks	215e908a11	Reworking of the VariantFiltration system to allow for a windowed view of variants and inclusion of more data to the various filters. This now allows us to incorporate both the clustered SNP filter and a SNP-near-indels filter, which otherwise wasn't possible. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1484 348d0f76-0448-11de-a6fe-93d51630548a	2009-08-31 02:16:39 +00:00