gatk3的最后一个经典版本3.8

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Eric Banks 0b73573abc Slightly modifying the way to use the IUPAC ambiguity codes in the FastaAlternateReferenceMaker. Previously it required you to create a single sample VCF and then to pass that in to the tool, but Geraldine convinced me that this was a pain for users (because they usually have multi-sample VCFs). Instead now you can pass in a multi-sample VCF and specify which sample's genotypes should be used for the IUPAC encoding. Therefore the argument changed from '--useIUPAC' to '--use_IUPAC_sample NA12878'.		2014-04-02 21:34:25 -04:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Slightly modifying the way to use the IUPAC ambiguity codes in the FastaAlternateReferenceMaker.	2014-04-02 21:34:25 -04:00
public	Slightly modifying the way to use the IUPAC ambiguity codes in the FastaAlternateReferenceMaker.	2014-04-02 21:34:25 -04:00
settings/helpTemplates	Replaced local drmaa and Jama artifacts with versions from maven central.	2014-02-22 01:21:35 +08:00
.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	Rename existing PipelineTests to QueueTests to prepare for upcoming push of new pipeline tests	2014-03-10 21:24:03 -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	Update pom versions to mark the start of GATK 3.2 development	2014-03-18 01:18:59 -04:00

README.md

The Genome Analysis Toolkit

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