.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH GMER_CALLER "1" "31 May 2018" "GenomeTester" "GenomeTester User Manuals"
.SH NAME
gmer_caller \- call the genotypes from a file with counted k-mers
.SH SYNOPSIS
.B gmer_caller
[\fI\,OPTIONS\/\fR] \fI\,<COUNTS_FILE>\/\fR
.SH OPTIONS 
.HP
\fB\-\-training_size\fR NUM \- Use NUM markers for training (default 100000)
.HP
\fB\-\-runs\fR NUMBER       \- Perform NUMBER runs of model training (use 0 for no training)
.HP
\fB\-\-num_threads\fR NUM   \- Use NUM threads (min 1, max 32, default 16)
.HP
\fB\-\-header\fR            \- Print table header
.HP
\fB\-\-non_canonical\fR     \- Output non\-canonical genotypes
.HP
\fB\-\-prob_cutoff\fR       \- probability cutoff for calling genotype (default 0)
.HP
\fB\-\-alternatives\fR      \- Print probabilities of all alternative genotypes
.HP
\fB\-\-info\fR              \- Print information about individual
.HP
\fB\-\-no_genotypes\fR      \- Print only summary information, not actual genotypes
.HP
\fB\-\-model\fR TYPE        \- Model type (full, diploid, haploid)
.HP
\fB\-\-params\fR PARAMS     \- Model parameters (error, p0, p1, p2, coverage, size, size2)
.HP
\fB\-\-coverage\fR NUM      \- Average coverage of reads
.HP
\fB\-D\fR                  \- increase debug level
.SH EXAMPLES
 You could find some usage examples in /usr/share/doc/genometester/README.FastGT.md
.SH "SEE ALSO"
 \fBglistquery\fR(1), \fBglistmaker\fR(1), \fBglistcompare\fR(1), \fBgmer_counter\fR(1)