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