gatk3的最后一个经典版本3.8

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Mauricio Carneiro e991307eb5 Including SplitByRG in the FullProcessingPipeline Why wasn't it there before, you ask ---------------------------------- Before I was running it separately (by hand), but now it's integrated in the FullProcessingPipeline. Integration was a pain because of Queue's limitation of only allowing 1 @Output file. This forced me to write the ugliest piece of code of my life, but it's working and it's processing the YRI from scratch using that right now. So I'm happy... somewhat. Other changes to the pipeline ----------------------------- * Add --filter_bases_not_stored to the IndelRealigner step -- sometimes BAM files have reads with no bases stored in the unmapped section (no idea why) but this disrupts the pipeline. * Change adaptor marking parameter to "dual indexed" instead of "pair-ended" -- for PCR Free data.		2013-08-18 00:51:32 -04:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Adding ability to use Ryan's PCR error modeling to the Haplotype Caller.	2013-08-16 01:53:04 -04:00
public	Including SplitByRG in the FullProcessingPipeline	2013-08-18 00:51:32 -04:00
settings	More detailed labels for arguments in the gakdocs (requested by David)	2013-08-16 14:25:53 -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/