Showing docs for version 3.7-0
BaseQualitySumPerAlleleBySample
Sum of evidence in reads supporting each allele for each sample
Category
Annotation Modules
VCF Field
FORMAT (sample genotype-level)
Type
StandardSomaticAnnotation
Overview
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.
Notes
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.
Caveats
- At this time, BaseQualitySumPerAlleleBySample can only be called from MuTect2