ZhiGroup / ROH-DICE

ROH-DICE

ROH-DICE (Runs of homozygous diplotype cluster enumerator) searches for clusters of ROH regions given a genotype panel (in compressed VCF format), minimum length in terms of the number of sites, and the number of samples.

Usage:

python ROH-DICE.py [-h] [-i INPUT] [-o OUTPUT] [-w MIN_SAMPLES] [-l MIN_LENGTH] [-L]

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input file in compressed (.gz) VCF format
  -o OUTPUT, --output OUTPUT
                        Your destination output file.
  -w MIN_SAMPLES, --min_samples MIN_SAMPLES
                        Minimum number of samples in each ROH cluster.
  -l MIN_LENGTH, --min_length MIN_LENGTH
                        Minimum number of sites in each ROH cluster.
  -L, --max_length      Maximize the number of sites in each cluster (by
                        default samples are maximized).
                        

Citation:

Ardalan Naseri, Degui Zhi, Shaojie Zhang (2024) Discovery of runs-of-homozygosity diplotype clusters and their associations with diseases in UK Biobank eLife 13:e81698 https://doi.org/10.7554/eLife.81698