Question: SNP scoring using PLINK
0
gravatar for GabrielMontenegro
5.0 years ago by
United Kingdom
GabrielMontenegro560 wrote:

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.

snp plink • 3.0k views
ADD COMMENTlink modified 10 weeks ago by Biostar ♦♦ 20 • written 5.0 years ago by GabrielMontenegro560
1
gravatar for Joey
5.0 years ago by
Joey410
Seattle
Joey410 wrote:

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 allelein your scoring file matches with either one of the alleles in the *.bim file.

 

-Joey

ADD COMMENTlink written 5.0 years ago by Joey410

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.
 

ADD REPLYlink written 5.0 years ago by GabrielMontenegro560

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.

ADD REPLYlink written 5.0 years ago by Joey410
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