Calculating PRS in a large cohort

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14 months ago

haasroni • 0

Hi everyone,

I have a merged vcf file with genotypes for a very large number of individuals. I have a list of SNPs and their weights that can be used to calculate the PRSs for a trait, and I want to calculate the PRSs using the large vcf file (can be converted to plink). Is there an efficient way to do that with PLINK, or any other software? Could anyone please help with a command for example?

Thank you!

PRS • 782 views

ADD COMMENT • link 14 months ago by haasroni • 0

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plink: https://choishingwan.github.io/PRS-Tutorial/plink/

ADD REPLY • link 14 months ago by size_t ▴ 120

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Thank you! Do you know if possible to give a score file (--score) that has chr and positions instead of SNP IDs?

ADD REPLY • link 14 months ago by haasroni • 0

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If anyone is wondering about the same thing, the discussion with the developer about this can be found here.

https://groups.google.com/g/plink2-users/c/FFoYaGoosRw/m/jM6eO2_VAAAJ?utm_medium=email&utm_source=footer

ADD REPLY • link 14 months ago by haasroni • 0

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