Gemma

Introduction

Gemma is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets.

For more information, please check its website: https://biocontainers.pro/tools/gemma and its home page on Github.

Versions

0.98.3

Commands

gemma

Module

You can load the modules by:

module load biocontainers
module load gemma

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Gemma on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=gemma
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers gemma

gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt \
    -gk -o mouse_hs1940

gemma -g ./example/mouse_hs1940.geno.txt.gz \
    -p ./example/mouse_hs1940.pheno.txt -n 1 -a ./example/mouse_hs1940.anno.txt \
    -k ./output/mouse_hs1940.cXX.txt -lmm -o mouse_hs1940_CD8_lmm