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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-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
  1. Each program can be run using a command line prompt allowing for each tuning parameter to be defined.
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