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Table 1 PLINK parameters for run of homozygosity (ROH) analysis

From: Identification of selection signatures involved in performance traits in a paternal broiler line

Parameter Value Definition
-homozyg-snp 50 Minimum number of SNP required to consider a ROH;
-homozyg-kb 300 Size (Kb) of the sliding window;
-homozyg-density 50 Minimum density required to consider a ROH;
-homozyg-gap 1000 Maximum size (Kb) between two SNP to be considered in the same ROH;
-homozyg-window-snp 50 Number of SNP present in the sliding window;
-homozyg-window-het 3 Number of heterozygous SNP allowed in a ROH;
-homozyg-window-missing 5 Number of missing calls allowed in a ROH;
-homozyg-window-threshold 0.05 Proportion of overlapping windows that must be called homozygous to define a given SNP as in a homozygous segment.