Showing docs for version 3.6-0 | The latest version is


Sum of evidence in reads supporting each allele for each sample

Category Annotation Modules

VCF Field FORMAT (sample genotype-level)

Type StandardSomaticAnnotation


In the domain of somatic variants, a variant call can be supported by a few high quality reads. The BaseQualitySumPerAlleleBySample annotation aims to give the user an estimate of the quality of the evidence supporting a variant.


BaseQualitySumPerAlleleBySample is called and used by MuTect2 for variant filtering. This annotation is applied to SNPs and INDELs. Qualities are not literal base qualities, but instead are derived from the per-allele likelihoods derived from the assembly engine.


  • At this time, BaseQualitySumPerAlleleBySample can only be called from MuTect2

Return to top

See also GATK Documentation Index | Tool Docs Index | Support Forum

GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.