readAllelicCountsFile: Read allelic counts file

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

Read allelic counts file

Description

Read file containing counts of ref and alt alleles of common Toolkit 4.

Usage

readAllelicCountsFile(file, format, zero = NULL)

Arguments

file	Input file containing counts of ref and alt alleles
format	File format. If missing, derived from the file extension. Currently only GATK4 CollectAllelicCounts (tsv) format supported.
zero	Start position is 0-based. Default is FALSE for GATK, TRUE for BED file based intervals.

Value

A CollapsedVCF with the parsed allelic counts.

Author(s)

Markus Riester

Examples

ac.file <- system.file("extdata", "example_allelic_counts.tsv", 
    package="PureCN")
vcf_ac <- readAllelicCountsFile(ac.file)

lima1/PureCN documentation built on April 24, 2024, 8:23 p.m.