chartl 47fa7e2227 + Added override to extractFileEntries ... + UG now doesn't care whether it's given SNPs or indels to genotype, it will do the right thing -- so remove the option to specify which GM user wants + Max misamatches argument removed integration test will follow git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5638 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-14 15:13:35 +00:00
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BatchMerge.q	+ Added override to extractFileEntries	2011-04-14 15:13:35 +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