MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis.

References:

• de Leeuw, Christiaan A., et al. "MAGMA: generalized gene-set analysis of GWAS data." PLoS Comput Biol 11.4 (2015): e1004219.

• MAGMA Main Site

• Module Name: magma (see the modules page for more information)
• Singlethreaded app
• Example files in /usr/local/apps/MAGMA/gene_location/

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load magma

[user@cn3144 ~]$ magma --annotate --snp-loc /usr/local/apps/MAGMA/gene_location/example.snp.txt \
--gene-loc /usr/local/apps/MAGMA/gene_location/NCBI37.3/NCBI37.3.gene.loc \
--out temp.test

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226

[user@biowulf ~]$

Create a batch input file (e.g. MAGMA.sh). For example:

#!/bin/bash
module load magma
magma --annotate --snp-loc /usr/local/apps/MAGMA/gene_location/example.snp.txt \
--gene-loc /usr/local/apps/MAGMA/gene_location/NCBI37.3/NCBI37.3.gene.loc \
--out temp.test

Submit this job using the Slurm sbatch command.

sbatch MAGMA.sh

Create a swarmfile (e.g. MAGMA.swarm). For example:

magma annotate --snp-loc snp1.txt --gene-loc NCBI37.3.gene.loc --out out1
magma annotate --snp-loc snp2.txt --gene-loc NCBI37.3.gene.loc --out out2
magma annotate --snp-loc snp3.txt --gene-loc NCBI37.3.gene.loc --out out3

Submit this job using the swarm command.

swarm -f MAGMA.swarm [-g #] [-t #] --module magma