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gatk3的最后一个经典版本3.8
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Eric Banks ea8a1edeb6 Adding option to CombineGVCFs to have it break blocks at every N sites. 
Using --breakBandsAtMultiplesOf N will ensure that no reference blocks span across
genomic positions that are multiples of N.  This is especially important in the
case of scatter-gather where you don't want your scatter intervals to start in the
middle of blocks (because of a limitation in the way -L works in the GATK for VCF
records with the END tag).

For example, running with --breakBandsAtMultiplesOf 5 on this record:
1       69491   .       G       <NON_REF>       .       .       END=69523       GT:DP:GQ:MIN_DP:MIN_GQ:PL       ./.:94:99:82:99:0,120,1800

Will produce the following records:
1       69491   .       G       <NON_REF>       .       .       END=69494       GT:DP:GQ:MIN_DP:MIN_GQ:PL       ./.:94:99:82:99:0,120,1800
1       69495   .       C       <NON_REF>       .       .       END=69499       GT:DP:GQ:MIN_DP:MIN_GQ:PL       ./.:94:99:82:99:0,120,1800
1       69500   .       T       <NON_REF>       .       .       END=69504       GT:DP:GQ:MIN_DP:MIN_GQ:PL       ./.:94:99:82:99:0,120,1800
etc.

Added docs and a new test.
 		2015-03-12 14:42:10 -04:00
licensing Updated license information 2014-10-14 17:10:12 -04:00
protected Adding option to CombineGVCFs to have it break blocks at every N sites. 2015-03-12 14:42:10 -04:00
public Log a warning if using incompatible arguments in DepthOfCoverage 2015-03-10 18:14:21 -04:00
settings/helpTemplates Output JSON version of docs for Galaxy 2014-10-09 06:42:25 -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 Added faster built executable, non-packaged jars. 2014-11-05 00:30:46 +08:00
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 Faster builds, with updates to documentation generation. 2014-11-05 00:32:23 +08:00

README.md

The Genome Analysis Toolkit

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