Mark DePristo 74e153ff4a FisherStrand now uses RankSumTest isUsableBase to decide if a read should be included in testing ... -- Previously used hardcoded MAPQ > 20 && QUAL > 20 but now uses isUsableBase -- Updating MD5s as appropriate		2012-07-18 16:07:47 -04:00
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bqsr	Enabled a whole other bunch of integration tests for BQSRv2. While I was there I also changed the default context size for indels to 3 (from 8) since that's what works best in the current implementation (as suggested by Ryan). At this point, all of the new core tools (ReduceReads, BQSRv2, HaplotypeCaller, UG extensions) have been moved over to protected and should be stable. Looks like we are pretty much ready for GATK 2.0!	2012-07-17 23:36:43 -04:00
compression/reducereads	Updating default value for -mindel to the one used by Khalid in the pipeline and me in my tests.	2012-07-10 02:04:26 -04:00
genotyper	FisherStrand now uses RankSumTest isUsableBase to decide if a read should be included in testing	2012-07-18 16:07:47 -04:00
haplotypecaller	Moving HaplotypeCaller integration and unit tests over to protected as well.	2012-07-17 14:51:26 -04:00