readAllelicCountsFile {PureCN} | R 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)

[Package PureCN version 1.22.2 Index]