This is a brand new tool to detect runs of homozygosity with many enhancements and portability to any platform..
Requires Java 8 or above. HTSJDK, Apache Commons-cli and FlafLAF are the 3 dependencies handled by maven.
git clone https://github.com/kelepiradam/ROHMMCLI.git
cd ROHMMCLI
./build.sh
Download source code from the release page and extract it to a folder. Run build.bat
Çelik, G., & Tuncalı, T. (2021). ROHMM—A flexible hidden markov model framework to detect runs of homozygosity from genotyping data. Human Mutation, 1–11. https://doi.org/10.1002/humu.24316