ReadStrelkaIDVCF: Read in the data lines of an ID VCF created by Strelka...

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

Description

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

Usage

ReadStrelkaIDVCF(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.

Value

A data frame storing data lines of the VCF file.

Note

In ID (small insertion and deletion) catalogs, deletion repeat sizes range from 0 to 5+, but for plotting and end-user documentation deletion repeat sizes range from 1 to 6+.

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