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Mutation Mapping Analysis Pipeline for Pooled RNA-Seq

Kyle Johnsen, Nathaniel Jenkins, Jonathon Hill


MMAPPR2 maps mutations resulting from pooled RNA-seq data from the F2 cross of forward genetic screens. Its predecessor is described in a paper published in Genome Research (Hill et al. 2013). MMAPPR2 accepts aligned BAM files as well as a reference genome as input, identifies loci of high sequence disparity between the control and mutant RNA sequences, predicts variant effects using Ensembl's Variant Effect Predictor, and outputs a ranked list of candidate mutations.

See vignette for instructions

Publication for the original MMAPPR

Installation Notes

MMAPPR2 depends on two system tools to function: Samtools and VEP. Both must be installed and in the PATH to be found by the appropriate functions.

Installing Samtools

Instructions to install samtools can be found at and installation instructions are in the INSTALL file included with samtools.

Installing VEP

You'll need Ensembl VEP, which you can install like this, replacing my_species with your species (e.g., danio_rerio):

git clone
cd ensembl-vep
perl -a ac -s {my_species}

This installs the most recent VEP and allows you to create a cache for your desired species, which is what MMAPPR2 expects by default. If you depart from the installation shown here, or if things don't go smoothly, see Ensembl's instructions and make sure any differences are accounted for in the VEPFlags object.

Note: If you have any trouble installing VEP, using their Docker image may save you a lot of hassle.

Note: We have found that R sometimes has issues finding VEP, especially when perlbrew is used. If you encounter errors at the path to your perl installation to the .Rprofile file. For example:

Sys.setenv(PATH=paste("/Path/to/Perlbrew", Sys.getenv("PATH"), sep=":"))