NAME¶

alleleCounts.pl - Generate tab seperated file with allelic counts and depth for each specified locus.

SYNOPSIS¶

Where possible use the C version for large data (it's also more configurable).

alleleCounts.pl

  Required:
    -bam      -b      BAM/CRAM file (expects co-located index)
                       - if CRAM see '-ref'
    -output   -o      Output file [STDOUT]
    -loci     -l      Alternate loci file (just needs chr pos)
                       - output is different, counts for each residue
  Optional:
    -ref      -r      genome.fa, required for CRAM (with colocated .fai)
    -minqual  -m      Minimum base quality to include (integer) [30]
    -mapqual  -q      Minimum mapping quality of read (integer) [35]
    -gender   -g      flag, presence indicates loci file to be treated as gender SNPs.
                       - cannot be used with 's'
    -snp6     -s      flag, presence indicates loci file is SNP6 format.
                       - cannot be used with 'g'
                       - changes output format
    -help     -h      This message
    -version  -v      Version number