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I have about 750 vcf files and I am looking to generate a Polygenic Risk Score for each individual. I am planning to use either PLINK or LDPhred to generate a Risk Score. I have phenotype information of these individuals.

Can anyone verify if the polygenic risk score is calculated using individual vcf files or should I look into combining the vcf files?

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  • $\begingroup$ What kind of polygenic risk score? For what diseases? What genes? Using which of the many approaches? $\endgroup$
    – terdon ♦
    Commented Aug 17, 2022 at 12:56

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For the tools you mentioned, you should convert to BED format. Other tools will accept VCF. It should work either way, combined or not, though you may have to adjust your pipeline depending on which you prefer. I'd imagine a combined file would be easier to work with.

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