vcfToIndelsClassification: VCF to Indels Classification

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

VCF to Indels Classification

Description

Convert a VCF file containing Indels into a data frame where each indel is classified as repet-mediated, Microhomology-mediated or other. A summary of the count of indels (deletions and insertions) and their proportion with respect to the total is also provided.

Usage

vcfToIndelsClassification(indelsVCF.file, sampleID, genome.v = "hg19")

Arguments

indelsVCF.file	path to input VCF (file must be tabix indexed). This file should have been already filtered for the final indels sets to be used in the analysis.
sampleID	name of the sample
genome.v	version of the genome to be used to look up the context of the indel, either "hg19", "hg38", "mm10" or "canFam3"

Value

the function returns a list with elements "indels_classified", which is a table with the indels and their classification, and "count_proportion", which is a summary of the count of indels and their proportion

Examples

res <- vcfToIndelsClassification("test.indel.vcf.gz","testSample","hg19")

Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.