I've been struggling with constructing a PRS score. In the pics you can see how my summary stats and my target data look like.

Target Data Summary Stats

I've tried the following code which should be pretty straightforward:

plink \
  --bfile target \
  --score summary_stats.txt 1 4 6 header \
  --out final

When I run it, I get this message:

10499994 variants and 1198 people pass filters and QC. Note: No phenotypes present.

The data is binary and the fam file really doesn't have phenotypes (it's -9). Is there any way to still run a PRS?

I'm unsure what I'm doing wrong and would really appreciate some insight! Also, the data has been harmonized already so it should technically work!

Summary Statistics My data

  • $\begingroup$ Please don't put images of text into posts. Copy-paste the actual text and add it as a code block. If formatting is difficult, someone else can edit the post to fix that up. $\endgroup$
    – gringer
    Dec 21, 2023 at 9:19

1 Answer 1


I'm a little confused about what you mean by there being no phenotype. To build the score you need a phenotype, although to apply it you might not. (Usually PRS is build with a base dataset and then applied using a target dataset). Here's a good tutorial about doing PRS in plink that might help you:


Also this paper is a really good paper that helped me better understand how building PRS works:


Hope this helps!


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