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).
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