gatk3的最后一个经典版本3.8

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Eric Banks 17eb7b49fe Adding ability to use Ryan's PCR error modeling to the Haplotype Caller. There is now a command-line option to set the model to use in the HC. Incorporated Ryan's current (unmerged) branch in for most of these changes. Because small changes to the math can have drastic effects, I decided not to let users tweak the calculations themselves. Instead they can select either NONE, CONSERVATIVE (the default), or AGGRESSIVE. Note that any base insertion/deletion qualities from BQSR are still used. Also, note that the repeat unit x repeat length approach gave very poor results against the KB, so it is not included as an option here.		2013-08-16 01:53:04 -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	Merge pull request #375 from broadinstitute/rp_queue_jobreport_rscript	2013-08-14 12:48:42 -07:00
settings	Rev picard to get optimized tribble feature reads	2013-08-02 10:31:36 -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/