rpoplin 7db9601c9d Checking in the 1000G phase1 cleaning and calling scripts for posterity's sake, but also to show everyone what the current best practices for VQSR training looks like. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5015 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-19 14:32:52 +00:00
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ASHGcalling.scala	By popular demand I'm adding the qscript I used to do the 660 bamfile 1000G calling for ASHG. It does cleaning, BAQing, and merging in 3mb chunks genome-wide then calls SNPs on those temporary bams.	2010-12-17 18:49:03 +00:00
MethodsDevelopmentCallingPipeline.scala	Use the sites-only HapMap files in the Methods development pipeline	2011-01-18 20:50:09 +00:00
Phase1Calling.scala	Checking in the 1000G phase1 cleaning and calling scripts for posterity's sake, but also to show everyone what the current best practices for VQSR training looks like.	2011-01-19 14:32:52 +00:00
Phase1Cleaning.scala	Checking in the 1000G phase1 cleaning and calling scripts for posterity's sake, but also to show everyone what the current best practices for VQSR training looks like.	2011-01-19 14:32:52 +00:00
variantRecalibrator.scala	At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.	2010-09-02 21:30:48 +00:00