MAGMA

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.

Documentation

The manual can be downloaded here. An additional brief overview of conditional, joint and interaction modelling can be found here.

The primary publication for MAGMA is:

de Leeuw C, Mooij J, Heskes T, Posthuma D (2015): MAGMA: Generalized gene-set analysis of GWAS data. PLoS Comput Biol 11(4): e1004219. doi:10.1371/journal.pcbi.1004219 (link)

When using MAGMA, please refer to this paper.

An in-depth statistical view of gene-set analysis in general can be found here:

de Leeuw C, Neale BM, Heskes T, Posthuma D (2016): The statistical properties of gene-set analysis. Nat Rev Genet 17(6): 353-64. doi:10.1038/nrg.2016.29 (link)

A detailed workflow and guideline for conditional, joint and interaction gene-set and gene property analyis can be found in this paper:

de Leeuw C, Stringer S, Dekkers IA, Heskes T, Posthuma D (2018): Conditional and interaction gene-set analysis reveals novel function pathways for blood pressure. Nat Commun 9(1): 3768. doi:10.1038/s41467-018-06022-6 (link)

For questions, comments, feedback and feature requests, contact Christiaan de Leeuw. To be kept informed about important program updates, you can also send an email to join the (low-traffic) mailing list.

Program and auxiliary files

Download links for the program itself as well as a number of auxiliary files can be found below. For Linux, binaries were compiled on Debian but will also usually run on other distributions. An additional statically linked binary is provided in case certain libraries cannot be found due to some difference in Linux distributions (typically an error message regarding a missing .dll file); using this may resolve the problem.

The MAGMA source code can also be downloaded below, which can be used to compile the program on the target system if this is not supported by the provided binaries (note that standard copyright applies; the MAGMA binaries and source code may not be distributed or modified).

A log of all the major changes in the latest version can be found here.

MAGMA v1.07b (updated 08/11/2016)
Operating systemCompilerLink
Linux (Debian, 64 bits)Intel / icpcDownload
Linux (Debian, 64 bits, static linking)Intel / icpcDownload
Windows (64 bits, static linking)MinGW-w64Download
Mac OS (64 bits)g++Download
Source code-Download

When you download MAGMA, we request that you subscribe to the (low-traffic) mailing list as well. This will keep you informed of any updates to the program and auxiliary files.

Supporting R scripts and documentation for performing post-hoc QC of gene set and interaction analysis results can be downloaded here.

Auxiliary files (updated 19/09/2018)

For the gene location files, gene locations for protein-coding genes were obtained from the NCBI site. Locations are defined as the region from transcription start site to transcription stop site. These location files contain Entrez gene IDs.

The SNP synonym file contains lists of synonymous SNP rs IDs that refer to the same SNP, up to date to dbSNP release 151. These synonyms can be included in MAGMA analyses to improve mapping of SNPs across different files, in particular SNP p-value files and reference data. The 1,000 Genomes reference data files below already include a data-specific synonym file.

Latest update: updated synonyms to dbSNP 151.

FileLink
Gene locations, build 38Download
Gene locations, build 37Download
Gene locations, build 36Download
SNP synonyms, dbSNP 151Download
Reference data (updated 19/09/2018)

The reference data files are created from Phase 3 of 1,000 Genomes. The SNP locations in the data are in reference to human genome Build 37. An additional file with definitions of the sub-populations is available as well, which can be used to extract specific sub-populations from the 1,000 Genomes data files. Data-specific SNP synonym files are included with the data.

Latest update: updated synonym files to dbSNP151, and mapped a block of ss IDs in .bim files on chromosome 12 to corresponding rs IDs.

PopulationFile SizeLink
European488 MBDownload
African1057 MBDownload
East Asian440 MBDownload
South Asian521 MBDownload
Middle/South American492 MBDownload
Sub-population definitions15 KBDownload
Original version (v1.0)

For reference, the binary and source code for the original version of MAGMA (v1.0) corresponding to the MAGMA paper from 2014 (see reference and link above) is available here. This version of MAGMA is released under the GPL v3.0 license; note that this license applies only to MAGMA v1.0, standard copyright applies to all subsequent versions of MAGMA.