ICAMS (version 3.0.11)

SplitListOfMutectVCFs: Split each Mutect VCF into SBS, DBS, and ID VCFs (plus VCF-like data frame with left-over rows)

Description

Split each Mutect VCF into SBS, DBS, and ID VCFs (plus VCF-like data frame with left-over rows)

Usage

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

Value

A list containing the following objects:

• SBS: List of VCFs with only single base substitutions.

• DBS: List of VCFs with only doublet base substitutions as called by Mutect.

• ID: List of VCFs with only small insertions and deletions.

• 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.

Arguments

list.of.vcfs

List of VCFs as in-memory data.frames.

suppress.discarded.variants.warnings

Logical. Whether to suppress warning messages showing information about the discarded variants. Default is TRUE.