hzAnalyzer: detection, quantification, and visualization of contiguous homozygosity in high-density genotyping datasets

Table 1 Comparison of segment overlap counts between hzAnalyzer and PLINK homozygous segment/runs-of-homozygosity detection routines

		Number of intersecting segments in other dataset
Dataset	Total segments	0	1	2	3-5	6-10	>10
hzAnalyzer	5,781	440	5,240	93	7	0	1
PLINK	8,040	30	5,059	1,777	1,108	66	0

Runs of homozygosity were detected using PLINK's default settings (ROH >1 Mb), and a corresponding set of homozygous segments with >1 Mb length selected from the complete hzAnalyzer dataset. The PLINK set was intersected with segments with ≥50 SNP/segment from the complete hzAnalyzer dataset, and the reverse intersection was performed between the hzAnalyzer (>1 Mb) and PLINK (>1 Mb) sets.

ISSN: 1474-760X