gatk-3.8

Author	SHA1	Message	Date
chartl	97e1a5262e	-ct x no longer includes coverage in the previous bin BatchMerge - additional support for indels (can't just test the alternate allele when it's an extended event, must also specify that you want to use the dindel model when you actually test the allele) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5300 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-24 15:52:04 +00:00
chartl	07d381ec51	BatchMerge now uses the correct UG settings, recently added by Eric ExpandIntervals now checks that identical intervals are not created by (un)fortunately-spaced targets VCFExtractIntervals no longer creates duplicate intervals in the case where a VCF has multiple entries at the same site git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5294 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-23 18:46:15 +00:00
chartl	851b3e71f9	Major revision of the batch merge script. All sites are now used, hooks for some UG settings, no longer reliant on the pipeline management library (pipeline libs are probably going to go away -- nobody uses them) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5241 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-14 23:52:05 +00:00
chartl	a463dbcda1	Refactoring the qscript directory; oneoffs, playground, and core git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5017 348d0f76-0448-11de-a6fe-93d51630548a	2011-01-19 15:23:40 +00:00