getAlleleCounts: Obtain allele counts for 1000 Genomes loci through external...

In Wedge-lab/battenberg: Battenberg subclonal copy number caller

Obtain allele counts for 1000 Genomes loci through external program alleleCount

Description

Obtain allele counts for 1000 Genomes loci through external program alleleCount

Usage

getAlleleCounts(
  bam.file,
  output.file,
  g1000.loci,
  min.base.qual = 20,
  min.map.qual = 35,
  allelecounter.exe = "alleleCounter"
)

Arguments

bam.file	A BAM alignment file on which the counter should be run.
output.file	The file where output should go.
g1000.loci	A file with 1000 Genomes SNP loci.
min.base.qual	The minimum base quality required for it to be counted (optional, default=20).
min.map.qual	The minimum mapping quality required for it to be counted (optional, default=35).
allelecounter.exe	A pointer to where the alleleCounter executable can be found (optional, default points to $PATH).

Author(s)

sd11

Wedge-lab/battenberg documentation built on April 5, 2025, 9:15 a.m.