VCFTools: Calculation of r^2 fails

Hello,

I have 9 pooled population samples with variants called into a VCF files. I merged the VCF files and tried to calculate r^2, and every site yields "-nan" and never an actual r^2 value.

How can I fix this, or maybe I should use another approach/tool?

Adrian

vcf vcftools r2

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updated 3.4 years ago by Ram

• written 12.1 years ago by Adrian Pelin

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