kshakir 95fc6c0a83 Changed VR tranches from old 0.1-10 to new 100 to 90. ... Using hapmap training and truth based on wiki. Explicitly setting the ts_filter_level even though 99.0 is the default. Recal file path now ends with with .recal. Added ar's vcf input. Omni rod name now omni instead of 1kg. The VR RodBind tags had spaces in them. Was passing both the full intervals and the chunk intervals to chunk jobs. Switched back to chr20 for default since the VR crashes on small intervals sets with "MESSAGE: Matrix is singular." Log files names based on the file paths + .out. Added eval statifications by sample based on the Hybrid Selection / Whole Exome pipeline. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5800 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-13 14:38:56 +00:00
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qscript	Changed VR tranches from old 0.1-10 to new 100 to 90.	2011-05-13 14:38:56 +00:00
src/org/broadinstitute/sting	Corrected memory handling and jobName formatting issues	2011-05-12 17:47:56 +00:00
test/org/broadinstitute/sting/queue	Moved some of the java to scala conversions from production to test code as it's not needed in production and slows down the code.	2011-05-05 04:11:15 +00:00