748787c509
helper script to the papuan processing... minor updates
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5489 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-22 14:11:02 +00:00
f6d4b0aaf5
Using an embedded version of Picard for merging un-indexed bam files after scatter/gather instead of requiring the QScripts to specify the picard JAR. May do this for the GATK jar too.
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Fixed initialization of pending counts when using -startFromScratch so the count doesn't start at zero and end at -<#njobs>.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5483 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-21 18:20:01 +00:00
96628457cb
pacbio calling pipeline also using VQSR2 now, minor updates on the other pipelines to get the papuans through.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5479 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-18 22:06:52 +00:00
55e5971b3b
this is a oneoff script to clean the papuans and test TargetCreator and IndelRealigner with scatter gathering.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5457 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-17 17:09:53 +00:00
carneiro
kshakir