gatk-3.8

gatk3的最后一个经典版本3.8

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ebanks 902cf84448 Bug fix: if the most likely allele frequency is 0, don't make a variant call (even if the Qscore for AF=1/n > threshold) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2033 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-13 04:10:32 +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	Better configuration support. Now supports everything that people have expressed interest in except edit distance.	2009-11-11 20:54:49 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	Bug fix: if the most likely allele frequency is 0, don't make a variant call (even if the Qscore for AF=1/n > threshold)	2009-11-13 04:10:32 +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	Better snpSelector, plus VCFmerge tool	2009-11-11 22:02:57 +00:00
scala/src	Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.	2009-11-02 06:02:41 +00:00
settings	Take 2, updating picard with bug fix for bam files containing no reads.	2009-11-12 22:52:08 +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	removed some extra debugging commands from the build.xml	2009-11-04 06:28:12 +00:00
ivy.xml	Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.	2009-11-02 06:02:41 +00:00