Type Members

1.  class EndRepairArtifactLikelihoodFilter extends SomaticVariantFilter with LazyLogging

   Filter that examines SNVs with the alt allele being A or T to see if they are likely the result of aberrant end-repair and A-base addition.

   Filter that examines SNVs with the alt allele being A or T to see if they are likely the result of aberrant end-repair and A-base addition.

   Occurs when end-repair is performed in a way that chews back single-stranded 3' overhangs to create a blunt end, but over-digests and ends up creating a recessed 3' end which subsequently (and incorrectly) gets filled in with one or more As during the A-base addition step. The result is one or more base substitutions to A at the 3' end of molecules, which after PCR also shows up as substitutions to T at the 5' end.

2.  class FilterSomaticVcf extends FgBioTool with LazyLogging

   Annotations

   @ClpAnnotation()

3.  trait SomaticVariantFilter extends AnyRef

   Trait for classes that can compute annotations on a somatic variant call and optionally apply one or more filters to the calls.