Split each Mutect VCF into SBS, DBS, and ID VCFs (plus two VCF-like data frame with left-over rows).
SplitListOfMutectVCFs(list.of.vcfs)List of VCFs as in-memory data.frames.
A list with 3 in-memory VCFs and two left-over VCF-like data frames with rows that were not incorporated into the first 3 VCFs, as follows:
SBS VCF with only single base substitutions.
DBS VCF with only doublet base substitutions
as called by Mutect.
ID VCF with only small insertions and deletions.
other.subs VCF like data.frame with
rows for coordinate substitutions involving
3 or more nucleotides, e.g. ACT > TGA or AACT > GGTA.
multiple.alternative.alleles VCF like data.frame with
rows for variants with multiple alternative alleles, for example
ACT mutated to both AGT and ACT at the same position.