ICAMS: SplitStrelkaSBSVCF – R documentation

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SplitStrelkaSBSVCF

Split an in-memory Strelka VCF into SBS, DBS, and variants involving > 2 consecutive bases

Description

SBSs are single base substitutions, e.g. C>T, A>G,.... DBSs are double base substitutions, e.g. CC>TT, AT>GG, ... Variants involving > 2 consecutive bases are rare, so this function just records them. These would be variants such ATG>CCT, AGAT>TCTA, ...

Usage

SplitStrelkaSBSVCF(vcf.df, max.vaf.diff = 0.02, name.of.VCF = NULL)

Arguments

`vcf.df`	An in-memory data frame containing a Strelka VCF file contents.
`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.

Value

A list of in-memory objects with the elements:

SBS.vcf: Data frame of pure SBS mutations – no DBS or 3+BS mutations.
DBS.vcf: Data frame of pure DBS mutations – no SBS or 3+BS mutations.
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.

ICAMS

In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

v2.3.10

GPL-3 | file LICENSE

Authors

Steve Rozen, Nanhai Jiang, Arnoud Boot, Mo Liu, Yang Wu

Initial release