getAlleleCounts: Obtain allele counts for 1000 Genomes loci through external...
In shaghayeghsoudi/Battenberg_customized: Battenberg subclonal copy number caller

Obtain allele counts for 1000 Genomes loci through external program alleleCount

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

`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).