gatk3的最后一个经典版本3.8

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Eric Banks 530e0e5ea6 Added a fix for combining/genotyping positions over spanning deletions. Previously, if a SNP occurred in sample A at a position that was in the middle of a deletion for sample B, sample B would be genotyped as homozygous reference there (but it's NOT reference - there's a deletion). Now, sample B is genotyped as having a symbolic DEL allele. Minor cleanup added. Note that I also removed Laura's previous fix for this problem. Existing integration tests change because I've added a new header line to the VCF being output. I also added several tests for the new functionality showing: 1. genotyping from separate and already combined gvcfs give the same output 2. genotyping over multiple spanning deletions works 3. combining works too Existing unit tests also cover this case.		2015-05-11 15:11:16 -04:00
licensing	Updated license information	2014-10-14 17:10:12 -04:00
protected	Added a fix for combining/genotyping positions over spanning deletions.	2015-05-11 15:11:16 -04:00
public	Added a fix for combining/genotyping positions over spanning deletions.	2015-05-11 15:11:16 -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/