18deeec6b0
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
|
||
|---|---|---|
| .. | ||
| VectorPairHMM | ||
| c | ||
| chainFiles | ||
| doc | ||
| external-example | ||
| gatk-framework | ||
| gatk-package | ||
| gatk-queue-extgen | ||
| gsalib | ||
| java/config | ||
| package-tests | ||
| perl | ||
| queue-framework | ||
| queue-package | ||
| repo | ||
| sting-root | ||
| sting-utils | ||
| pom.xml | ||