jmaguire e2780c17af Checkin of the Multi-Sample SNP caller. ... Doesn't work yet; same command I used to use now causes GATK to throw an exception. Will check with Matt & Aaron tomorrow, then do a regression test. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1509 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-03 00:23:28 +00:00
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examples	Update naming for consistency.	2009-06-30 22:03:21 +00:00
gatk	Checkin of the Multi-Sample SNP caller.	2009-09-03 00:23:28 +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	Converts from fastq.gz to unaligned BAM format. Accepts a single fastq (for single-end run) or two fastqs (for paired-end run). Also allows you to set certain BAM metadata (read groups, etc.).	2009-08-27 20:20:09 +00:00
utils	Checkin of the Multi-Sample SNP caller.	2009-09-03 00:23:28 +00:00