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

BMC Genomics

Table 3 Top Recommendations for Detecting Autozygosity

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

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).

ISSN: 1471-2164