A number of additional features has been implemented in MAGMA, more fully described in ‘Supplemental Methods—Extensions’. Gene analysis can be expanded with a gene-environment interaction component, which can subsequently be carried over to the gene-set analysis. Options for aggregation of rare variants and for fixed-effects meta-analysis for both gene and gene-set analysis are also available. Efficient SNP to gene annotation and a batch mode for parallel processing are provided to simplify the overall analysis process. MAGMA is distributed as a standalone application using a command-line interface. The C++ source code is also made available, under an open source license. MAGMA can be downloaded from http://ctglab.nl/software/magma.
