Start /end of genes in plink (.bim , .bed , .fam) files
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6.0 years ago
marwa.cs91 ▴ 30

Hello all, I am new in plink analysis, 

How can I search in plink files for location (start / end)of gene for example CD2AP gene in which its location on chromosome 6: base pairs 47,477,745 to 47,627,262

Thanks in advance

genes plink .bim .fam .bed • 1.7k views
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6.0 years ago

I think you're looking for the --make-set command in plink:

http://pngu.mgh.harvard.edu/~purcell/plink/dataman.shtml#makeset

Given a file of genes in this format:

Chromosome start end ID

Plink will give you a file with a set of SNPs located in that range for each gene in your input list

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