depristo cd293f145b More stable reduced reads representation. Bug fixes throughout. No diffs by <1% of sites in an exome, and the majority of these differences are filtered out, or are obvious artifacts. UnitTests for BaseCounts. BaseCounts extended to handle indels, but not yet enabled in the consensus reads. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5939 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-03 20:11:31 +00:00
..
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	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	More stable reduced reads representation. Bug fixes throughout. No diffs by <1% of sites in an exome, and the majority of these differences are filtered out, or are obvious artifacts. UnitTests for BaseCounts. BaseCounts extended to handle indels, but not yet enabled in the consensus reads.	2011-06-03 20:11:31 +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rpoplin	Removed unused importants, but some of these scripts are now out of date (they have been for a long time) so they don't compile anyway	2011-05-22 18:43:48 +00:00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