Single Nucleotide Polymorphisms SNP genotypes are usually encoded as 0, 1 or 2, based on the number of copies of non-reference alleles. E.g., suppose a SNP has reference allele G,. "/>

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Plink2 tutorial houses for rent by owner only tactical fat guy If your variants have been left-normalized and split, and your single-letter allele codes are restricted to {A, C, G, T, a, c, g, t}, the SNP counts reported by PLINK 2.0 and bcftools should be identical..

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