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gatk-3.8/java/test/org/broadinstitute/sting/gatk/walkers/phasing
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fromer 92cf7744a6 Set minMQ = max(minMQ, minBQ) for phasing since anyway we cap BQ by MQ; also, lowered MIN_BASE_QUALITY_SCORE for phasing to 17 (was previously 20) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4781 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-12-03 16:31:13 +00:00
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MergeMNPsIntegrationTest.java As per Eric and Mark's suggestions, separated the segregating MNP merger (MergeMNPs) from the more general merger employed for annotation purposes (MergeSegregatingAlternateAlleles). Both use the same core MergePhasedSegregatingAlternateAllelesVCFWriter 2010-12-01 16:42:08 +00:00
MergeSegregatingAlternateAllelesIntegrationTest.java As per Eric and Mark's suggestions, separated the segregating MNP merger (MergeMNPs) from the more general merger employed for annotation purposes (MergeSegregatingAlternateAlleles). Both use the same core MergePhasedSegregatingAlternateAllelesVCFWriter 2010-12-01 16:42:08 +00:00
ReadBackedPhasingIntegrationTest.java Set minMQ = max(minMQ, minBQ) for phasing since anyway we cap BQ by MQ; also, lowered MIN_BASE_QUALITY_SCORE for phasing to 17 (was previously 20) 2010-12-03 16:31:13 +00:00