Calling mutations from MA lines

accuMUlate is a mutation caller designed with Mutation Accumulation (MA) experiments in mind. The probablistic approach to mutation calling implemented by accuMUlate allows us to identify putative mutations, accommodate noise produced by NGS sequencing, and accommodate diploid, haploid or diploid to haploid experimental designs.

The preprint is available on bioRxiv accuMUlate: A mutation caller designed for mutation accumulation experiments

Getting started

The wiki gives a detailed account of how to prepare your data, compile accuMUlate, run the program and understand the results. If you want to get started even more quickly here's what you need to know.

Prerequisites

In order to install accuMUlate you will need the following libraries

• BamTools
• Eigen
• Boost::program_options

You will also need CMake to manage the build. Package managers for linux distributions and OS X should let you instal pre-compiled versions of Eigen, Boost and CMake. The wiki describes how to compile BamTools. If you want to run the program's unit tests you also need GTest, but this is not a requirement to get the software running.

Compilation

With prerequisites installed, building the software is easy:

cd build
cmake ..
make

Test run

The above commands should make two programs in the build directory: accuMUlate (the mutation caller) and denominate (a tool for calculating the number of callable sites in a BAM file). To test that everything has gone well you can run these on some test data. First accuMUlate, running from the working directory this should produce a warning message and detailed information about one possible mutation:

build/accuMUlate -c test/data/example_params.ini \
             -b test/data/test.bam \
             -r test/data/test.fasta \
             -i test/data/test.bed 

Warning: excluding data from 'D6' which is included in the BAM file but not the list of included samples
good_mutation	600	601	C	D1	CC->G	0.999999	0.999999	1	1.86137e-10	137	13	11	0	011.8531	-0.756908	1	1	

And then denominate, the mysterious string of integers are the number of ancestrally "A", "C", "G" and "T" bases for each sample that could be called for a mutation if one was present.

build/denominate -c test/data/example_params.ini \
            -b test/data/test.bam \
            -r test/data/test.fasta \
            -i test/data/test.bed \
            --max-depth 150

Warning: excluding data from 'D6' which is included in the BAM file but not the list of included samples
2	1	0	0	2	1	0	0	2	1	0	0	2	1	0	0	2	1	0   0	

How it works

The accuMUlate model is described in. Long et al. Low base-substitution mutation rate in the germline genome of the ciliate Tetrahymena thermophila. Genome Biology and Evolution 8: 3629-39 (2016). doi: https://doi.org/10.1093/gbe/evw223

Help, bugs, and suggestions

Your first stop should be the wiki, which contains information about the input and output files and more detail about using accuMUlate. If that doesn't help please file issues at this repository or email David Winter.