gatk3的最后一个经典版本3.8

Mark DePristo 2d35065238 QualityByDepth remaps QD values > 40 to a gaussian around 30 ... -- This is a temporarily fix / hack to deal with the very high QD values that are generated by the haplotype caller when nearby events occur within reads. In that case, the QUAL field can be many fold higher than normal, and results in an inflated QD value. This hack projects such high QD values back into the good range (as these are good variants in general) so they aren't filtered away by VQSR. -- The long-term solution to this problem is to move the HaplotypeCaller to the full bubble calling algorithm -- Update md5s		2013-03-14 16:09:41 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	QualityByDepth remaps QD values > 40 to a gaussian around 30	2013-03-14 16:09:41 -04:00
public	Merge pull request #104 from broadinstitute/eb_fix_output_annotation_GSA-837	2013-03-14 12:52:00 -07:00
settings	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Fix tests that were consistently or intermittently failing when run in parallel on the farm	2013-03-06 13:56:54 -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	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00