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"
)

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).

sd11