gatk3的最后一个经典版本3.8

Go to file

Eric Banks 672fbe437e Various updates for KB, mostly so that reviews through IGV work properly. 1. Fix for the -okayToMiss argument for indels. In cases where we make calls with different alleles, it wasn't allowing us to skip the site for FNs. 2. Need to add confidence and isComplexEvent attributes to the equality and duplicate checks in MVC. 3. Treat unknown confidences as reviewed for now. We need this until IGV gets updated to use confidences for reviews.		2013-07-21 21:20:05 -04:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Last feature request from Reich/Paavo labs: the allSitePLs feature in UG worked but not quite filled requirements. What's needed is the ability to have all 10 PLs for EVERY site, regardless of whether they are variant or not. Previous version only emitted the 10 PLs in reference sites. Problem is that, if all PLs are emitted in all sites and every single site is quad-allelic (only way to have the PLs printed out in a valid way) then the ability to filter variants and to use the INFO fields may be compromised.	2013-07-18 12:54:52 -04:00
public	GATK engine: add ability to do on-the-fly BAM file sample renaming at runtime	2013-07-18 15:48:42 -04:00
settings	Rev picard, sam-jdk, tribble, and variant to version 1.91.1453	2013-05-07 14:21:15 -04:00
.gitignore	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
README.md	Update README file for the 2.6 release	2013-06-20 13:08:29 -04:00
build.xml	build.xml: make ant -p output only important build targets	2013-07-19 14:35:00 -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
ivy.xml	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00

README.md

The Genome Analysis Toolkit

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