zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk3的最后一个经典版本3.8
13,605 Commits
1 Branch
0 Tags
257 MiB
Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
Go to file
Valentin Ruano-Rubio d363725b4b Adds support for omniploidy to GenotypeGVCFs and CombineGVCFs. 
Same changes fixed the problem for GenotypeGVCFs and CombineGVCFs.

Stories:

  - https://www.pivotaltracker.com/story/show/77626044
  - https://www.pivotaltracker.com/story/show/77626854

Changes:

  - Generalized the code for the merging in GATKVariantContextUtils to cope
    with ploidy != 2.
  - GenotypeGVCFs now check that the input's ploidy conform to the '-ploidy'
    argument.
  - Moved out Refernce Confidence VC merging code from GATKVariantContextUtils
    so that we can keep new code in protected.

Caveats:

  - GenotypeGVCFs only can deal with input files that have the same ploidy in
    all positions; the one that the user MUST indicate in the -ploidy argument
    (if different to the default 2).
  - CombineGVCFs won't necessarely complain if its passed mixed ploidy
    inputs but you won't be able to genotype it with GenotypeGVCFs.

Test:

   - Removed deprecated unit tests for GATKVariantContextUtils.
   - Moved unit-tests regarding GVCF merging from GATKVariantContextUtilsUnitTest
     to ReferenceConfidenceVariantContextUtilsUnitTest.
   - Added unit test for new code for mapping genotype indices between allele
     index encoding in GenotypeLikelihoodCalculator.
   - GenotypeGVCFs and CombineGVCFs original integration test are unaffected
     by the change.
   - Added tetraploid run integration tests to check on non-diploid execution
     of GenotypeGVCFs and CombineGVCFs.
 		2014-09-02 15:06:47 -04:00
licensing deleted old license files 2013-07-02 16:36:47 -04:00
protected Adds support for omniploidy to GenotypeGVCFs and CombineGVCFs. 2014-09-02 15:06:47 -04:00
public Adds support for omniploidy to GenotypeGVCFs and CombineGVCFs. 2014-09-02 15:06:47 -04:00
settings/helpTemplates Various documentation improvements 2014-07-14 12:03:03 -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 Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -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 3.3 development 2014-07-17 12:09:33 -04:00

README.md

The Genome Analysis Toolkit

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