Software: Gemma
Description
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.
Available Versions
| Unspecified: | 0.98.3 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/gemma and its home page on Github.
Commands
- gemma
Module
You can load the modules by:
module load biocontainers
module load gemma
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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