carneiro 36db9bdcd5 Implemented and tested BWA alignment in the data processing pipeline. ... caveat: Right now bwa only supports one read group, so if the original file had multiple @RG lines, only the first one will be kept. (working on a solution to this) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5931 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-02 23:03:07 +00:00
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carneiro	Implemented and tested BWA alignment in the data processing pipeline.	2011-06-02 23:03:07 +00:00
chartl	Moving this script out of playground while I figure out what's going on.	2011-05-23 17:48:44 +00:00
delangel	Script to run UG to create annotated all-pop VCF files to use for Phase1 VQSR indel project consensus. Paralleles and generalizes SNP version, so in theory this script can be used for both SNP and Indel consensus.	2011-05-25 16:50:59 +00:00
depristo	removing dependance on jobQueue == gsa	2011-05-27 10:12:09 +00:00
fromer	Add CNV sub-dir	2011-06-02 21:47:13 +00:00
hanna	Incorporating Khalid's feedback.	2011-04-08 16:22:49 +00:00
kshakir	Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.	2011-03-24 14:03:51 +00:00
rpoplin	Removed unused importants, but some of these scripts are now out of date (they have been for a long time) so they don't compile anyway	2011-05-22 18:43:48 +00:00
QTools.q	Generalized association is now working. Output is in a horrific format. Implementation of T-testing. Improvements are to look for classes dynamically (a la VariantEval/VariantAnnotator), beautify output, and do optimizations where they exist.	2011-03-01 01:23:37 +00:00