Start /end of genes in plink (.bim , .bed , .fam) files

Question

[marwa.cs91]

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

Answer 1

[Philipp Bayer]

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