This tool can be used to find common haplotype regions in a dataset of half-siblings and their parents.
It requires PLINK and Snakemake to run.
Different config files should be used depending on the input data density. For WGS data, config/high_density.yaml should be used.
For less dense data, config/medium_density.yaml can be used. These can also be manually adjusted.
The input should be in plink-friendly format - .bim, .bed and .fam.
The output consists of a table and graph. The graph shows homozygous regions, linked regions and overlaps