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.IX Title "ALLELECOUNTER 1p"
.TH ALLELECOUNTER 1p "2022-09-30" "perl v5.34.0" "User Contributed Perl Documentation"
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.SH "NAME"
alleleCounts.pl \- Generate tab seperated file with allelic counts and depth for each specified locus.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Where possible use the C version for large data (it's also more configurable).
.PP
alleleCounts.pl
.PP
.Vb 1
\&  Required:
\&
\&    \-bam      \-b      BAM/CRAM file (expects co\-located index)
\&                       \- if CRAM see \*(Aq\-ref\*(Aq
\&    \-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 \*(Aqs\*(Aq
\&    \-snp6     \-s      flag, presence indicates loci file is SNP6 format.
\&                       \- cannot be used with \*(Aqg\*(Aq
\&                       \- changes output format
\&    \-help     \-h      This message
\&    \-version  \-v      Version number
.Ve