AF column in VCF file
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10 weeks ago
Eliza • 0

Hi , I'm new to genetics . I have a VCF file and for each sample I need to identify if it is heterozygous or homozygous. For example, if AF=0.5 is it herto or homo?

Thank you

VCF AF heterozygous • 170 views
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10 weeks ago
iraun 5.7k

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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