Than you for your answer . As I understand you can encode hetro as 1 and homozygous as 2 . And if the SNP is not present then the it is encoded as 0 .I was wondering if this genotype encoding is based on minor if major allele? Since I want to preform a SKAT test and I have to build a genotype matrix: numeric genotype matrix with each row as a different individual and each column as a separate gene/snp. Each genotype should be coded as 0, 1, 2, and 9 for AA, Aa, aa, and missing, where A is a major allele and a is a minor allele. So if I base my encoding on the AF field and say that 0.5 is hetro is it ok ?
AF column in VCF file
1 answer
AF stands for "Allele frequency". 0.5 means heterozygous. Another way of checking the zygosity is the GT field, standing for genotype. There you will see things like 1/1 = Homozygous for the alternative allele (the variant); 0/1 = heterozygous; 0/0 = homozygous for the reference allele (no variant).
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