gatk3的最后一个经典版本3.8

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Mauricio Carneiro 725656ae7e Generalizing the FullProcessingPipeline Qscript We have generalized the processing script to be able to handle multiple scenarios. Originally it was designed for PCR free data only, we added all the steps necessary to start from fastq and process RNA-seq as well as non-human data. This is our go to script in TechDev. * add optional "starting from fastq" path to the pipeline * add mark duplicates (optionally) to the pipeline * add an option to run with the mouse data (without dbsnp and with single ended fastq) * add option to process RNA-seq data from topHat (add RG and reassign mapping quality if necessary) * add option to filter or include reads with N in the cigar string * add parameter to allow keeping the intermediate files		2013-11-07 16:34:29 -05:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Merge pull request #413 from broadinstitute/rp_qd_and_qual_updates_in_ref_model_pipeline	2013-11-05 06:33:17 -08:00
public	Generalizing the FullProcessingPipeline Qscript	2013-11-07 16:34:29 -05:00
settings	Modify gatkdoc template to handle downsampling info better	2013-09-26 14:50:32 -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	Resolving warnings	2013-09-23 12:42:22 -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	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/