gatk3的最后一个经典版本3.8

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Ron Levine 645d418015 Changed hardcoded downsampling max/min coverage values to parameters Rename parameters using camel case and add to integration test Correct documentation for maxReadsInRegionPerSample and minReadsPerAlignmentStart Change the argument--minReadsPerAlignmentStart in the integration test from 50 to 5 'each genomic location' only pertains to minReadsPerAlignmentStart, not maxReadsInRegionPerSample		2014-10-09 17:09:26 -04:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Changed hardcoded downsampling max/min coverage values to parameters	2014-10-09 17:09:26 -04:00
public	This warning message actually happens all the time in AssessNA12878 when we subset down to biallelic events but I've verified that it is working as intended. Moving the logging level up to debug.	2014-09-29 11:40:38 -04:00
settings/helpTemplates	changed the GATKDocs format to PHP	2014-08-18 18:04:07 -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	Now passing in the path to the GATK directory to tests.	2014-09-02 01:40:59 +08:00

README.md

The Genome Analysis Toolkit

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