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This is the wiki for the burden_testing repository, nicknamed MUMMY, which contains a software suite for running rare variant aggregation tests from next-generation sequencing data. It started out as a collection of perl scripts wrapping the MONSTER software. It was used in this configuration to run the analyses for this article and this one. This early version was mostly written by Daniel Suveges (@DSuveges) and has been released as v1.0, available for download in the releases section. In this configuration, it is a "MONSTER wrapper", hence the nickname.
In order to maximise compatibility and ease of deployment, we have packaged the software in a singularity container. We have also added support for a second software, SMMAT, which is described in this article. Like MONSTER, SMMAT allows fitting a mixed model, thereby taking into account fine population structure and other random effects. It also has an efficient implementation that makes it orders of magnitude faster to run than MONSTER.
MUMMY simplifies running SMMAT and MONSTER, in that it takes care of all the format conversions for you. It also writes genome-wide gene set files and performs variant selection for every gene according to the selection and weighting criteria of your choosing.
- First, head over to the installation page
- Prepare your data
- Then, read about the three pipelines you can run using this software.
- Run the analysis!