Table 1 ROH Detection Parameters
Program | Parameters | Code | Parameters Used |
|---|---|---|---|
PLINK | Varied Parameters: - Heterozygote allowance - SNP threshold to call a ROH - Sliding window size in SNPs - Missing SNP allowance - Window threshold to call a ROH Fixed Parameters: - Sliding window size in kb - Kb threshold to call a ROH - Minimum SNP density to call a ROH - Maximum gap before splitting ROH | --homozyg-window-het --homozyg-snp --homozyg-window-snp --homozyg-window-missing --homozyg-window-threshold --homozyg-window-kb --homozyg-kb --homozyg-density (kb) --homozyg-gap (kb) | 0/1 15/25/50/75/100/200/350/500 Same as SNP threshold (5% of SNP threshold) (0.05% of SNP threshold) 0 (unused) 0 (unused) 5, 000 (set high to ignore) 5, 000 (set high to ignore) |
GERMLINE | Varied Parameters: - Mismatching heterzygote allowance - Minimum ROH length (in cM or Mb) - Window size in SNPs Fixed Parameters: - Mismatching homozygote allowance | -err_het -min_m (in cM) -bits -err_hom | 0/1 0.15/0.25/0.5/0.75/1/2/3.5/5 Expected number of SNPs for given cM length 0 |
BEAGLE | Varied Parameters: - Non-HBD to HBD transition rate - HBD to non-HBD transition rate Fixed Parameters: None | nonhbd2hbd = hbd2nonhbd = | 0.0001/0.01/0.1 0.25/0.5/1 |