|ALLELECOUNTER(1p)||User Contributed Perl Documentation||ALLELECOUNTER(1p)|
alleleCounts.pl - Generate tab seperated file with allelic counts and depth for each specified locus.
Where possible use the C version for large data (it's also more configurable).
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)  -mapqual -q Minimum mapping quality of read (integer)  -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