Calculating PRS in a large cohort

0

Entering edit mode

2.3 years 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 • 1.2k views

ADD COMMENT • link 2.3 years ago by haasroni • 0

1

Entering edit mode

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

ADD REPLY • link 2.3 years ago by size_t ▴ 120

0

Entering edit mode

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 2.3 years ago by haasroni • 0

0

Entering edit mode

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 2.3 years ago by haasroni • 0

Login before adding your answer.