code for calling mutatons from MA lines
C++ CMake Python Shell
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Modules
test
third-party/bamtools
utils
.travis.yml
CMakeLists.txt
LICENSE
README.md
main.cc
model.cc
model.h
params.ini
parsers.cc
parsers.h
run_tests.sh

README.md

Build Status DOI

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.

Required libs

Needs to be compiled/on path:

Provided in this repo * bamtools headers (for bamtools-utils, not in the normal include headers)

Compilation

At present 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.