R: Split a list of in-memory Strelka SBS VCF into SBS, DBS, and...

SplitListOfStrelkaSBSVCFs

R Documentation

Split a list of in-memory Strelka SBS VCF into SBS, DBS, and variants involving > 2 consecutive bases

Description

SBSs are single base substitutions, e.g. C>T, A<G,.... DBSs are double base substitutions, e.g. CC>TT, AT>GG, ... Variants involving > 2 consecutive bases are rare, so this function just records them. These would be variants such ATG>CCT, AGAT>TCTA, ...

Usage

SplitListOfStrelkaSBSVCFs(
  list.of.vcfs,
  suppress.discarded.variants.warnings = TRUE
)

Arguments

`list.of.vcfs`	A list of in-memory data frames containing Strelka SBS VCF file contents.
`suppress.discarded.variants.warnings`	Logical. Whether to suppress warning messages showing information about the discarded variants. Default is TRUE.

Value

A list of elements as follows:

SBS.vcfs: List of data.frames of pure SBS mutations – no DBS or 3+BS mutations.
DBS.vcfs: List of data.frames of pure DBS mutations – no SBS or 3+BS mutations.
discarded.variants: Non-NULL only if there are variants that were excluded from the analysis. See the added extra column discarded.reason for more details.