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Split a mixed-mutation VCF into SBS / DBS / ID sub-tables

Source: R/split_vcf.R
split_vcf.Rd

Classifies each row by REF/ALT length alone:

  • SBS (single base substitution): nchar(REF) == 1 && nchar(ALT) == 1

  • DBS (double base substitution): nchar(REF) == 2 && nchar(ALT) == 2

  • ID (indel): nchar(REF) != nchar(ALT)

  • Other (e.g. 3+bp substitutions): discarded with a recorded reason.

Usage

split_vcf(vcf, name_of_vcf = NULL)

Arguments

vcf

A VCF as a data.frame / data.table with at least REF and ALT columns.

name_of_vcf

Optional VCF name used in warning / error messages.

Value

A list with elements

  • SBS: data.table of SBS rows.

  • DBS: data.table of DBS rows.

  • ID: data.table of indel rows.

  • discarded: data.table of rows that did not fit any of the above, with a discarded.reason column — NULL when no rows were discarded.

Details

This is caller-agnostic. In particular, mSigSpectra does not merge adjacent SBSs into DBSs based on VAF similarity (which ICAMS did via SplitOneVCF for Strelka-style VCFs). Users who want that behavior should apply it as a post-processing step with their own VAF column.