Table 4.
Overview of parameters evaluated for the detection of ROHs using PLINK
| Test setting | Parameter | Tested range | Description |
|---|---|---|---|
| 1 | homozyg-window-snp | 20—150 (interval 10) | scanning window size—number of SNPs a scanning window contains |
| 1 | homozyg-window-threshold | based on homozyg-window-snp | scanning window threshold—proportion of overlapping windows that must be homozygous to define a given SNP as part of a homozygous segment |
| 2 + 3 | homozyg-snp | 20—150 (interval 10) | min. number of SNPs per ROH—minimal number of SNPs per ROH |
| 2 + 3 | homozyg-kb | based on homozyg-snp | min. ROH length [kb]—minimal desired length of a ROH in kb |
| 2 + 3 | homozyg-density | 0.04–0.2 (interval 0.04) | min. inverse density [kb/SNP]—on average a ROH must have at least 1 SNP per the defined number of kb |
| 2 + 3 | homozyg-gap | 50, 100, 250, 500, 1000 | max internal gap [kb]—max interval below that two SNPs are considered adjacent. If two SNPs within a segment are too far apart, the segment is split |
| 4 | homozyg-window-het | 0,1,2,3 | max. number of heterozygous SNPs per window |
| 4 | homozyg-window-missing | 3,5,7 | max. number of missing SNPs per window |