GMER_CALLER(1) | GenomeTester User Manuals | GMER_CALLER(1) |
gmer_caller - call the genotypes from a file with counted k-mers
gmer_caller [OPTIONS] <COUNTS_FILE>
--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
You could find some usage examples in /usr/share/doc/genometester/README.FastGT.md
glistquery(1), glistmaker(1), glistcompare(1), gmer_counter(1)
31 May 2018 | GenomeTester |