MMAPPR2

Mutation Mapping Analysis Pipeline for Pooled RNA-Seq

Kyle Johnsen, Nathaniel Jenkins, Jonathon Hill

Introduction

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, and outputs a ranked list of candidate mutations.

See vignette for instructions

Publication for the original MMAPPR

Installation Notes

MMAPPR2 depends on Samtools to function. It must be installed and in the PATH to be found by the appropriate functions.

Installing Samtools

Instructions to install samtools can be found at https://github.com/samtools/samtools and installation instructions are in the INSTALL file included with samtools.