kshakir 08c13f3944 Using embedded GATK. ... Hardcoded the reference and dbsnp since the training rods are also hardcoded, for now. Changed freeze/chr20 to wg/chr20/cent1 to also test the heaviest known shard. Other cleanup. TODO: Memory command line options or have the script figure it out using FLS or similar. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5799 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-12 23:19:49 +00:00
..
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	Using embedded GATK.	2011-05-12 23:19:49 +00:00