ebanks 9b1d7921e8 added filter based on concordance to another call set ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1432 348d0f76-0448-11de-a6fe-93d51630548a		2009-08-18 15:16:30 +00:00
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examples	Update naming for consistency.	2009-06-30 22:03:21 +00:00
gatk	added filter based on concordance to another call set	2009-08-18 15:16:30 +00:00
indels	change paths to new ones	2009-07-24 07:28:43 +00:00
piecemealannotator	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
somaticcoverage	Cleanup: GATKEngine no longer needs to be lazy loaded, b/c the plugin directory no longer exists.	2009-07-21 18:50:51 +00:00
tools	A very simple standalone filter for fooling around with the data: can extract only mapped or only unmapped reads, only reads with mapping quals > X, reads with average base qual > Y, reads with min base qual > Z, reads with edit distance from the ref > MIN and/or < MAX	2009-08-12 20:28:51 +00:00
utils	Now GenomicMap maps (and RemapAlignment outputs) regions between intervals on the master reference as 'N' cigar elements, not 'D'. 'D' is now used only for bona fide deletions.	2009-08-11 21:10:17 +00:00