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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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David Roazen 8b29030467 Change default downsampling coverage target for the HaplotypeCaller to 250 
-was previously set to 30, which seems far too aggressive given that with
 ActiveRegionWalkers, as with LocusWalkers, this limits the depth of any
 pileup returned by LIBS

-250 is a more conservative default used by the UG

-can adjust down/up later based on further experiments (GSA-699 will
 remain open)

-verified with Ryan that all integration test differences are either
 innocent or represent an improvement

GSA-699
 		2013-02-26 09:33:25 -05:00
..
annotator Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
beagle Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
bqsr PrintReads writes a header when used with -BQSR 2013-02-14 22:19:14 -05:00
compression/reducereads Fixing the failing RR integration tests. 2013-02-06 12:40:56 -05:00
diagnostics walker to calculate per base coverage distribution 2013-02-07 16:33:05 -05:00
diffengine Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
fasta Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
filters Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
genotyper Change default downsampling coverage target for the HaplotypeCaller to 250 2013-02-26 09:33:25 -05:00
haplotypecaller Change default downsampling coverage target for the HaplotypeCaller to 250 2013-02-26 09:33:25 -05:00
indels Fixed IndelRealigner reference length bug (GSA-774) 2013-02-19 16:00:36 -05:00
phasing Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
validation Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
varianteval Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
variantrecalibration Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
variantutils Replace org.broadinstitute.variant with jar built from the Picard repo 2013-02-05 17:24:25 -05:00