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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 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.
In order to run the containerised version, the only thing you will need is a recent (>v3.0) version of the Singularity software. Installation instructions can be found here.
In order to install the container, run :
singularity pull shub://hmgu-itg/burden_testing
Then interact with the container, e.g.:
singularity exec burden_testing_latest.sif help
More details on how the software is packaged can be found here.
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