depristo 165befd38a V1 of the post processing QC plotting scala script and R function. The scala script runs VariantEval on a VCF file, and computes QC metrics. The R script generates the report. Will discuss usage with data processing group. Ryan -- please add your additional plotting routines to this script, as you see fit. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5980 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-13 17:06:42 +00:00
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carneiro	Subversion crashed my intellij BADLY, so now moving the data processing pipeline to core in 2 steps.	2011-06-02 23:31:24 +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	Intermediate commit of indel consensus VQSR script, a couple of new features added, not for general use	2011-06-06 13:27:02 +00:00
depristo	V1 of the post processing QC plotting scala script and R function. The scala script runs VariantEval on a VCF file, and computes QC metrics. The R script generates the report. Will discuss usage with data processing group. Ryan -- please add your additional plotting routines to this script, as you see fit.	2011-06-13 17:06:42 +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rpoplin	Removed unused importants, but some of these scripts are now out of date (they have been for a long time) so they don't compile anyway	2011-05-22 18:43:48 +00:00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