gatk3的最后一个经典版本3.8

asivache ef00ba3ced added IndelGenotyperV2Walker ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1937 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-29 20:07:31 +00:00
R	R script for selecting a variety of baits (using %GC content and normalized coverage) for Nanostring assessment from those used in the Agilent whole exome hybrid selection design.	2009-09-22 18:10:14 +00:00
c	Fixed epic memory leak.	2009-10-29 16:32:43 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	Genotyper reimplemented. Does the same thing, at least for now, but internal data structures redesign enables collecting various statistics for indel-containing/reference-matching reads. The statistics are not yet used by the caller itself to make a better judgement w.r.t. the validity of the calls it makes, but they are now printed into the output stream (--verbose). The statistics (for both normal and tumor) include: indel observation count/total coverage, av. number of mismatches per indel-containing and per ref-matching read, av. mapping quality, av. mismatch rate and av. base quality within an NQS windoew around the indel, numbers of indel and ref observations per strand.	2009-10-29 19:09:16 +00:00
packages	added IndelGenotyperV2Walker	2009-10-29 20:07:31 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	simple monitor for watching pilot 1 call progress	2009-10-06 13:04:53 +00:00
scala/src	Major code refactoring:	2009-10-20 14:58:04 +00:00
settings	Bumping version of Picard for firehose compatibility.	2009-10-16 19:38:56 +00:00
shell	Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one!	2009-09-04 12:39:06 +00:00
testdata	GSA-182: Adding support for BED interval files.	2009-10-06 02:45:31 +00:00
build.xml	changes to the variation class, updates to SSG, updated tests based on changes to the SSGenotypeCall, and added the ability to run a single integration test from using the build script.	2009-09-10 04:31:33 +00:00
ivy.xml	Delete duplicate jgrapht reference.	2009-10-29 17:38:01 +00:00