Question: GWAS Make bed file from fam and bim and Polygenic Risk Score calculation
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gravatar for landscape95
6 months ago by
landscape95160
landscape95160 wrote:

Hi everyone, previously I had a set of bed/bim/fam file in Plink format for GWAS, now I have separate a set of Discovery and Target Samples for Polygenic Risk Score analysis. However, if I select individuals from the .fam file, the bed file will not be suitable for this set of bed/bim/fam file anymore. Does anyone know how to create a new bed file from bim and fam file or am I doing the right way?

Your help is really appreciated!

plink gwas • 339 views
ADD COMMENTlink modified 6 months ago by zx87547.7k • written 6 months ago by landscape95160
1

I don't understand the question. Please clarify. If this is about Plink formats, then:

  • bim is a map file for variants, like chr, pos...
  • fam is a phenotype file, FID, IID, sex, status...
  • bed is a binary genotype file, which is completely useless without having related above bim and fam files.

We cannot create new bed file from bim and fam.

ADD REPLYlink written 6 months ago by zx87547.7k

thank you, that's about Plink format.

ADD REPLYlink written 6 months ago by landscape95160

I have another question, in this case how can I make a Target sample data set, I already had the id of the Discovery and Target set from the total samples which I have in the set of bed/bim/fam file? Thank you very much!

ADD REPLYlink modified 6 months ago • written 6 months ago by landscape95160
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