SplitOneVCF: Split a VCF into SBS, DBS, and ID VCFs, plus a list of other...
In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Split a VCF into SBS, DBS, and ID VCFs, plus a list of other mutations

1	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 `ReadVCF`.
`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.
`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

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