SNP scoring using PLINK

Question

[GabrielMontenegro]

I am using the --score command in plink to estimate profiles for individuals based on an allelic scoring system.

The input file is just three columns with SNP name, reference allele and the score. However I am getting this message in the log file.

Warning: 3 lines skipped in --score file.

So I guess the first SNPs are not being read by plink? Change files but still same problem. Anyone has experience something similar?

Thank you.

Answer 1

[Joey]

Can you do two double checks:

a) Check if those SNPs are present in your genetic data (bed/bim/fam)?

and

b) If they are present, the reference allele in your scoring file matches with either one of the alleles in the *.bim file.

-Joey

[GabrielMontenegro]

Yes, I had a problem with the reference alleles on the bim files. That solved the problem.

If you have some experienced with the scoring function could you explain me what this two variables mean? I can't understand the definition from the plink manual explanation. Thank you again.

[Joey]

We have some papers where we used the genetic risk score in a Mendelian randomization study. Which variables do you want me to explain? I will try my best.