kshakir 475ad1259d Put a band-aid on the FCP by switching use of DINDEL to INDEL and explicitly running UG the old way with just indels and just snps. ... Switched YAML parser to new Broad parser which will additionally update picard cleaned bams to the latest version if the project and sample are specified. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5634 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-14 02:22:31 +00:00
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BatchMerge.q	Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.	2011-03-24 14:03:51 +00:00
FullCallingPipeline.q	Put a band-aid on the FCP by switching use of DINDEL to INDEL and explicitly running UG the old way with just indels and just snps.	2011-04-14 02:22:31 +00:00
MultiFullCallingPipeline.scala	Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.	2011-03-24 14:03:51 +00:00
recalibrate.scala	Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.	2011-03-24 14:03:51 +00:00
wgs.q	Whole genome pipeline script. currently chunks, cleans, calls, merges, selects and filters indels, recalibrates, and evals.	2011-04-13 16:59:48 +00:00