Split a mutect2 VCF into SBS, DBS, and ID VCFs, plus a list of other mutations
SplitOneMutectVCF(vcf.df)An in-memory data.frame representing a Mutect VCF, including
VAFs, which are added by ReadMutectVCF.
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)
and rows for complex indels.
multiple.alt 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.