Arnav
Call variants using a site-specific binomial model.
The methods underlying Arnav are described in this preprint.
arnav uses the Rmath libraries for the pbinom function and uses cereal for serializing C++ objects and storing them to disk.
Install
git clone --recursive https://github.com/gatoravi/arnav
mkdir build && cd build && cmake .. && make
Quickstart
A workflow describing how arnav can be used to detect putative somatic mutations in RNA sequencing data is described here.
Usage
List all options available with arnav
./arnav
Estimate site-specific priors for a list of sites specified in a bed file
./arnav prior-dump-fixed samples_readcountfile_list.tsv merged_priors.dump list_of_regions.bed.gz
To call mutations using the merged priors
./arnav call-using-merged sample_readcountfile_list.tsv merged_priors.dump
For details on the file-formats used in the steps above please see the Workflow section below.