gatk3的最后一个经典版本3.8

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Ami Levy-Moonshine c5fc5c4f8c create 2 new tools: - ASEReadCounter (public tool) replce Tuuli's script to produce the input to Manny's tool. It count the number of reads that support the ref allele and the alt allele, filtereing low qual reads and bases and keep only properPaired reads - ASECaller (private tool) take both RNA and DNA, and produce ontingencyTables still under development minor changes in other tools: - update RNA HC variant calling scala script - expose FS method pValueForContingencyTable to be able to call it from ASEcaller In ASEReadCounter: - allow different option to deal with overlaping read from the same fragment - add option to ignore or include indels in the pileups - add option to disabled DuplicateRead add ASEReadCounterIntegrationTest.java and files for the test		2015-03-21 16:56:00 -04:00
licensing	Updated license information	2014-10-14 17:10:12 -04:00
protected	create 2 new tools:	2015-03-21 16:56:00 -04:00
public	create 2 new tools:	2015-03-21 16:56:00 -04:00
settings/helpTemplates	Output JSON version of docs for Galaxy	2014-10-09 06:42:25 -04:00
.gitignore	Fixed bug using GraphBased due to infinite likelihoods resulting from the calculation of alignment cost of very long insertion or deletions (done in linear scale)	2014-04-01 16:14:52 -04:00
README.md	Update README file for the 2.6 release	2013-06-20 13:08:29 -04:00
ant-bridge.sh	Added faster built executable, non-packaged jars.	2014-11-05 00:30:46 +08:00
intellij_example.tar.bz2	Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)	2012-09-27 11:04:56 -04:00
pom.xml	Faster builds, with updates to documentation generation.	2014-11-05 00:32:23 +08:00

README.md

The Genome Analysis Toolkit

See http://www.broadinstitute.org/gatk/