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

Description

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

SplitListOfVCFs(
  list.of.vcfs,
  variant.caller,
  max.vaf.diff = 0.02,
  num.of.cores = 1,
  suppress.discarded.variants.warnings = TRUE
)

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.

list.of.vcfs: List of VCFs as in-memory data.frames.
variant.caller: Name of the variant caller that produces the VCF, can be either "strelka", "mutect", "freebayes" or "unknown". If variant caller is "mutect", do not merge SBSs into DBS.
max.vaf.diff: The maximum difference of VAF, default value is 0.02. If the absolute difference of VAFs for adjacent SBSs is bigger than max.vaf.diff, then these adjacent SBSs are likely to be "merely" asynchronous single base mutations, opposed to a simultaneous doublet mutation or variants involving more than two consecutive bases.
num.of.cores: The number of cores to use. Not available on Windows unless num.of.cores = 1.
suppress.discarded.variants.warnings: Logical. Whether to suppress warning messages showing information about the discarded variants. Default is TRUE.