rpoplin 20f29e4690 In the Methods development pipeline the call confidence threshold must be lowered from the default value for lowpass calling. What a bone-headed mistake! ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4941 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-05 20:30:55 +00:00
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qscript	In the Methods development pipeline the call confidence threshold must be lowered from the default value for lowpass calling. What a bone-headed mistake!	2011-01-05 20:30:55 +00:00
src	PrivatePermutations generalized to compute transition counts and average probabilities (and thus was renamed). Changes in some pipelines to reflect the change. Bugfix in the batch merging pipeline (it would halt because the allele VCF for genotyping batches could become off-spec).	2010-12-22 15:16:15 +00:00
test/org/broadinstitute/sting/queue	Updated pipeline test to match Eric's changes in r4846.	2010-12-17 19:52:09 +00:00