You may also want to review regions of homozygosity within a sample. Opal’s Regions of Homozygosity (ROH) viewer is designed to highlight whether your genome contains any large (>1MB) regions of homozygosity. Such regions could represent biological features such as consanguinity, uniparental disomy, or large deletions. It will also pick up on artifacts of VCF generation that could merit further investigation.
It displays information about large runs of homozygosity in two forms:
- A graphic, displaying the fraction of homozygous variants along the length of all chromosomes. This is a direct visualization of the information present in your uploaded VCF.
- A table, displaying calculated Runs of Homozygosity. Opal can display regions which are at least 1 MB, 3 MB, or 5MB in size with a density of homozygous variants of at least 75%. The 75% is set to allow for sequencing errors. The precise start and end points of the runs are approximate only.