kshakir 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. ... 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
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dataProcessing.scala	pacbio calling pipeline also using VQSR2 now, minor updates on the other pipelines to get the papuans through.	2011-03-18 22:06:52 +00:00
dataProcessingV2.scala	now merging bam files per sample and processing according to cleaning options.	2011-03-18 21:31:29 +00:00
justClean.scala	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.	2011-03-21 18:20:01 +00:00
pbCalling.scala	pacbio calling pipeline also using VQSR2 now, minor updates on the other pipelines to get the papuans through.	2011-03-18 22:06:52 +00:00