rpoplin 20f29e4690 In the Methods development pipeline the call confidence threshold must be lowered from the default value for lowpass calling. What a bone-headed mistake! ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4941 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-05 20:30:55 +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	In the Methods development pipeline the call confidence threshold must be lowered from the default value for lowpass calling. What a bone-headed mistake!	2011-01-05 20:30:55 +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