Table 1 Overview of parameter settings for SNP filtering and ROH detection with PLINK Custom PLINK parameter settings PLINK_A and PLINK_B adjusted to our investigated dataset for efficient subsequent ROH calling are displayed
Tool | Parameters | PLINK_A | PLINK_B |
|---|---|---|---|
Vcftools | minDP | 6 | 6 |
maxDP | 95 | 95 | |
max-missing-count | 15 | 15 | |
PLINK | homozyg-snp | 20 | 120 |
homozyg-kb | 1.6 | 9.93 | |
homozyg-density | 0.08 | 0.08 | |
homozyg-gap | 1000 | 1000 | |
homozyg-window-snp | 20 | 120 | |
homozyg-window-threshold | 0.25 | 0.04 | |
| Â | homozyg-window-missing | 5 | 5 |
homozyg-window-het | 1 | 1 |