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
13,319 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 18deeec6b0 Addresses issue with strict validation on GVCF files. 
More concretelly Picard's strict VCF validation does not like that there is alternative alleles that are not participating in any genotype call across samples.

This is an issue with GVCF in the single-sample pipeline where this is certainly expected with <NON_REF> and other relative unlikely alleles.

To solve this issue we allow the user to exclude some of the strict validations using a new argument --validationTypeToExclude. In order to avoid the validation
issue with GVCF the user needs to add the following to the command line: '--validationTypeToExclude ALLELES'

Story:

    https://www.pivotaltracker.com/story/show/68725164

Changes:

    - Added validateTypeToExclude argument to ValidateVariants walker.
    - Implemented the selective exclusion of validation types.
    - Added new info and improved existing documentation of the ValidateVariants walker.

Tests:

    - ValidateVariantsIntegrationTest#testUnusedAlleleError
    - ValidateVariantsIntegrationTest#testUnusedAlleleFix
 		2014-04-04 14:37:10 -04:00
licensing deleted old license files 2013-07-02 16:36:47 -04:00
protected Addresses issue with strict validation on GVCF files. 2014-04-04 14:37:10 -04:00
public Addresses issue with strict validation on GVCF files. 2014-04-04 14:37:10 -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/