Split a VCF into SBS, DBS, and ID VCFs, plus a list of other mutations
Split a VCF into SBS, DBS, and ID VCFs, plus a list of other mutations
SplitOneVCF(vcf.df, max.vaf.diff = 0.02, name.of.VCF = NULL)
vcf.df |
An in-memory data.frame representing a VCF, including
VAFs, which are added by |
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
|
name.of.VCF |
Name of the VCF file. |
A list with 3 in-memory VCFs and discarded variants that were not incorporated into the first 3 VCFs:
* 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.
* 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.
@md
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