getContextsSv: Determine SV type and length

In UMCUGenetics/mutSigExtractor: Extracts SNV, indel, DBS, and SV signatures from vcf files.

Determine SV type and length

Description

Determine SV type and length

Usage

getContextsSv(df, sv.caller = "gridss", return.raw = F, verbose = F)

Arguments

df	A dataframe containing the columns: chrom, pos, ref, alt, filter, id, info
sv.caller	Only applies when mode=='sv'. At this moment supports 'manta','manta_bnd, 'gridss', or 'pcawg'. Currently there is no standard to how SVs are reported in vcfs. Therefore, output from different callers will need to be parsed separately.
verbose	Print progress messages?

Value

A dataframe in the same structure as a bed file with an extra column stating the context of each variant

UMCUGenetics/mutSigExtractor documentation built on Aug. 30, 2024, 2:12 p.m.