gatk3的最后一个经典版本3.8

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Eric Banks c7e08965d0 The QD normalization for indels was busted and is now fixed. It is true that indels of length > 1 have higher QUALS than those of length = 1. But for the HC those QUALS are not that much higher, and it doesn't continue scaling up as the indels get larger. So we no longer normalize by indel length (which massively over-penalizes larger events and effectively drops their QD to 0). For the UG the previous normalization also wasn't perfect. Now we divide the indel length by a factor of 3 to make sure that QD is consistent over the range of indel lengths. Integration tests change because QD is different for indels. Also, got permission from Valentin to archive a failing test that no longer applies. Thanks to Kurt on the GATK forum for pointing this all out.		2014-01-13 15:23:36 -05:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	The QD normalization for indels was busted and is now fixed.	2014-01-13 15:23:36 -05:00
public	Write a new tool for spliting reads that have N cigar string.	2014-01-01 22:21:36 -05:00
settings	Rev'ing the Variant jar to incorporate some patches to the BCF encoder that Menachem needs.	2014-01-02 23:33:17 -05:00
.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	Separate tests that access the knowledge base from other tests	2013-12-06 11:31:35 -05:00
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	Changing from scala 2.9.2 to 2.10.2.	2013-09-23 12:42:22 -04:00

README.md

The Genome Analysis Toolkit

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