NAME

       gmer_caller - call the genotypes from a file with counted k-mers

SYNOPSIS

       gmer_caller [OPTIONS] <COUNTS_FILE>

OPTIONS

       --training_size NUM - Use NUM markers for training (default 100000)

       --runs NUMBER       - Perform NUMBER runs of model training (use 0 for no training)

       --num_threads NUM   - Use NUM threads (min 1, max 32, default 16)

       --header            - Print table header

       --non_canonical     - Output non-canonical genotypes

       --prob_cutoff       - probability cutoff for calling genotype (default 0)

       --alternatives      - Print probabilities of all alternative genotypes

       --info              - Print information about individual

       --no_genotypes      - Print only summary information, not actual genotypes

       --model TYPE        - Model type (full, diploid, haploid)

       --params PARAMS     - Model parameters (error, p0, p1, p2, coverage, size, size2)

       --coverage NUM      - Average coverage of reads

       -D                  - increase debug level

EXAMPLES

        You could find some usage examples in /usr/share/doc/genometester/README.FastGT.md

SEE ALSO

        glistquery(1), glistmaker(1), glistcompare(1), gmer_counter(1)

GenomeTester                                       31 May 2018                                    GMER_CALLER(1)