gatk3的最后一个经典版本3.8

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Ryan Poplin 0127799cba Reads are now realigned to the most likely haplotype before being used by the annotations. -- AD,DP will now correspond directly to the reads that were used to construct the PLs -- RankSumTests, etc. will use the bases from the realigned reads instead of the original alignments -- There is now no additional runtime cost to realign the reads when using bamout or GVCF mode -- bamout mode no longer sets the mapping quality to zero for uninformative reads, instead the read will not be given an HC tag		2014-06-30 10:35:50 -04:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Reads are now realigned to the most likely haplotype before being used by the annotations.	2014-06-30 10:35:50 -04:00
public	Reads are now realigned to the most likely haplotype before being used by the annotations.	2014-06-30 10:35:50 -04:00
settings/helpTemplates	Replaced local drmaa and Jama artifacts with versions from maven central.	2014-02-22 01:21:35 +08:00
.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	Fixed minor pom.xml line that was out of place after sortpom.	2014-06-26 01:01:19 +08:00

README.md

The Genome Analysis Toolkit

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