4 Commits (4f7a64a79853863473a0ea1e0912db08b327ad3c)

Author	SHA1	Message	Date
depristo	27d4b317fc	Simple program that calls indels in CEU trio exomes and WGS can compared the results. Overall the indel calls really look good to me, given reasonably good input BAM files. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6006 348d0f76-0448-11de-a6fe-93d51630548a	2011-06-16 12:56:04 +00:00
depristo	d77f4ebe31	CalibrateGenotypeLikelihoods now emits a molten data set with REF and ALT alleles, so that GL calibration can be evaluated as a function of the REF/ALT bases. DigestTable is a stand-alone Rscript that digests the multi-GB molten data table into a tiny table that shows reported vs. empirical GLs, as a function of a variety of features of the data, like REF/ALT, comp GT, eval GT, and GL itself. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5833 348d0f76-0448-11de-a6fe-93d51630548a	2011-05-21 14:02:30 +00:00
depristo	75db4705ab	Added splitContextByReadGroup() and fixed bug in getPileupForReadGroup() that resulted in a NPE when no reads where present for a read group. ... Added doc string for getNBoundRodTracks() Intermediate commit for CalibrateGenotypeLikelihoods and GenotypeConcordanceTable, so I have a record of my work. Not ready for public consumption. Really looking forward to making local commits so I can track my progress without needing to push incomplete functionality up to the server. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5807 348d0f76-0448-11de-a6fe-93d51630548a	2011-05-15 17:36:07 +00:00
depristo	5e9c0d00c6	Simple R script to visualize geontype likelihood accuracy ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5805 348d0f76-0448-11de-a6fe-93d51630548a	2011-05-14 15:05:55 +00:00