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Table 3 Top Recommendations for Detecting Autozygosity

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

Autozygosity Detection SNP data Top Program Chosen parameters
Within the past 20 generations Low genotyping error PLINK - Moderate LD-pruning
- 50 SNP threshold
- No heterozygote allowed
Within the past 20 generations High genotyping error PLINK - Moderate LD-pruning
- 45 SNP threshold
- No heterozygote allowed
Within the past 50 generations Low genotyping error PLINK - Light LD-pruning
- 65 SNP threshold
- No heterozygote allowed
Within the past 50 generations High genotyping error PLINK - Moderate LD-pruning
- 35 SNP threshold
- No heterozygote allowed
  1. Low genotyping error = 0.2% genotyping error rate. High genotyping error = 1% genotyping error rate. Moderate LD-pruning = Removal of SNPs within a 50 SNP window that had VIF greater than 2 (i.e. --indep 50 5 2 in PLINK). Light LD-pruning = Removal of SNPs within a 50 SNP window that had VIF greater than 10 (i.e. --indep 50 5 10 in PLINK).
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