gatk3的最后一个经典版本3.8

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Eric Banks 5b087c9897 Changed the functionality of the physical phasing in the HC: now hom vars are output as 0\|1. We do this for technical reasons, mostly because we don't genotype in the HC anymore; it's all done downstream by GenotypeGVCFs so we can't be sure that the genotype will be hom var. Also, there are steps in the downstream pipeline where genotypes can change, so assuming anything in the HC is a bad idea, and if we have phasing info in the het state, we want to propagate that forward. Now, PGT tag fixing happens downstream in GenotypeGVCFs. While I was in there I also cleaned up the code a bit and fixed a bug where annotation was happening before genotype creation when using the --includeNonVariantSites argument. Added tests accordingly.		2014-08-25 21:40:14 -04:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Changed the functionality of the physical phasing in the HC: now hom vars are output as 0\|1.	2014-08-25 21:40:14 -04:00
public	Disable physical phasing for non-diploid HC calling.	2014-08-23 10:52:07 -04:00
settings/helpTemplates	Various documentation improvements	2014-07-14 12:03:03 -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	Update pom versions to mark the start of GATK 3.3 development	2014-07-17 12:09:33 -04:00

README.md

The Genome Analysis Toolkit

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