readAllelicCountsFile: Read allelic counts file

View source: R/readAllelicCountsFile.R

readAllelicCountsFileR Documentation

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 Sept. 17, 2024, 5:48 a.m.