depristo 7272fcf539 Now uses the NO_HEADER option to avoid breaking MD5s due to changes in GATKArgumentCollection ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5518 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-26 12:00:37 +00:00
..
config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	Added support for a general GATK option --simplifyBAM to automatically remove and simplify kept reads in an output BAM file. Specifically, duplicate, non-PF, and unmapped reads are removed, and all extended tags in the retained SAM records are removed except the RG:Z tag. This option is very useful when creating temporary BAM files (merged per-population or multi-sample cleaned) for future calling (as in the 1000G processing pipeline). Results in a significant reduction in space of the resulting BAM, faster reading of the BAM, and surprisingly even faster UG performance:	2011-03-26 01:21:35 +00:00
test	Now uses the NO_HEADER option to avoid breaking MD5s due to changes in GATKArgumentCollection	2011-03-26 12:00:37 +00:00