---
name: "gmer_caller"
section: "1"
platform: "linux"
package: "genometester"
version: "4.0+git20200511.91cecb5+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmer_caller"
---

# gmer\_caller(1)

call the genotypes from a file with counted k-mers

## 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)](/glistquery/1.md), [**glistmaker**(1)](/glistmaker/1.md), [**glistcompare**(1)](/glistcompare/1.md), [**gmer\_counter**(1)](/gmer_counter/1.md)