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Table 1 ROH Detection Parameters

From: Detecting autozygosity through runs of homozygosity: A comparison of three autozygosity detection algorithms

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-density (kb)
--homozyg-gap (kb)
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
-min_m (in cM)
Expected number of SNPs for given cM length
BEAGLE Varied Parameters:
- Non-HBD to HBD transition rate
- HBD to non-HBD transition rate
Fixed Parameters: None
nonhbd2hbd =
hbd2nonhbd =
  1. Each program can be run using a command line prompt allowing for each tuning parameter to be defined.