ROH Caller

Regions of homozygosity (ROH) are detected as part of the small variant caller. The caller detects and outputs the runs of homozygosity from whole genome calls on autosomal human chromosomes. Sex chromosomes are ignored. ROH output allows downstream tools to screen for and predict consanguity between the individual’s parents.

The ROH algorithm runs on the small variant calls. It excludes variants with multi-allelic sites, indels, complex variants, non PASS filtered calls, and homozygous reference sites. The variant calls are then filtered further using a blacklist bed, and finally depth filtering is applied after the blacklist filter. The default value for the fraction of filtered calls is 0.2, filtering the calls with the highest 10% and lowest 10% in DP values. The resulting calls are then used to find regions.

A region is defined as consecutive variant calls on the chromosome with no large gap in between these variants. In other words, regions are broken by chromosome or by large gaps with no SNV calls. The gap size is set to 3 Mbases.