SplitListOfMutectVCFs: Split each Mutect VCF into SBS, DBS, and ID VCFs (plus...

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

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
)

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.

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.

ICAMS documentation built on April 3, 2021, 5:07 p.m.