gatk3的最后一个经典版本3.8

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Phillip Dexheimer b348ce8f25 Added -disableOptimizations argument to HaplotypeCaller. * This argument is intended to be used in conjunction with -bamout, and disable early-exit optimizations to allow reference regions to be contained in the output bam * Also forcibly includes the reference haplotype in the set of haplotypes given to the BAMWriter * Made -dontTrimActiveRegions visible, as it is likely also desirable in this use case * Addresses PT 77731660		2014-10-16 21:11:20 -04:00
licensing	Updated license information	2014-10-14 17:10:12 -04:00
protected	Added -disableOptimizations argument to HaplotypeCaller.	2014-10-16 21:11:20 -04:00
public	Throw UserException if input VCFs have duplicate samples but no genotypemergeoption is specified	2014-10-15 16:03:10 -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	Refactored maven directories and java packages replacing "sting" with "gatk".	2014-05-19 17:36:39 -04:00
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	Now passing in the path to the GATK directory to tests.	2014-09-02 01:40:59 +08:00

README.md

The Genome Analysis Toolkit

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