Calling mutations from MA lines
accuMUlate is a mutation caller designed with Mutation Accumulation (MA)
experiments in mind. Up until recently the software has been developed with the
goal of studying a specific MA experiment,
but we are in the process of adapting the program to work on any MA dataset you might have.
Please contact us if you are interested in using the software while we develop it.
Needs to be compiled/on path:
Provided in this repo
* bamtools headers (for bamtools-utils, not in the normal include headers)
cmake handles a basic build. Presuming bamtools and eigein are on
your path you can do this
cmake . make ./accuMUlate -c example/test_params.ini -b example/test.bam -r example/test.fasta -o example/test.out ./pp -c example/pp_params.ini -b example/test.bam -i example/test.out
The last line will run the caller on a test dateset with 6 000 bases, and show find mutations in each gene.