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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core	Adding another example call set to GATK resource bundle for use in VQSR wiki tutorial	2011-05-05 21:16:33 +00:00
examples	When /etc/mailname is unreadable fall back to the hostname.	2011-04-11 20:22:44 +00:00
lib	Thanks to mark: VCFInfoToTable removed in favor of a more flexible walker. Slight change to the argument structure of the walker to make it play more nicely with Queue: the field list parsing is pushed into the command line system (e.g. the variable is exposed as a List<String> and not a String, so Queue doesn't have to join a list into a string only to have it broken out again. This also allows the user to specify -F field1 -F field2 -F field3 if he/she so desires.	2010-12-15 03:33:36 +00:00
oneoffs	oops, putting the script back into a sensible state	2011-05-04 20:17:05 +00:00
playground	Changed VR tranches from old 0.1-10 to new 100 to 90.	2011-05-13 14:38:56 +00:00