ReadStrelkaSBSVCF: Read in the data lines of an SBS VCF created by Strelka...

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

Description

Read in the data lines of an SBS VCF created by Strelka version 1

Usage

ReadStrelkaSBSVCF(file, name.of.VCF = NULL)

Arguments

file	The name/path of the VCF file, or a complete URL.
name.of.VCF	Name of the VCF file. If NULL(default), this function will remove all of the path up to and including the last path separator (if any) in file and file path without extensions (and the leading dot) will be used as the name of the VCF file.
suppress.discarded.variants.warnings	Logical. Whether to suppress warning messages showing information about the discarded variants. Default is TRUE.

Value

A data frame storing data lines of a VCF file with two additional columns added which contain the VAF(variant allele frequency) and read depth information.

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