Is it possible to map Snps to genes given .bim/.fam/.bed files

Question

[apilarmoreno4]

Hi,

I was wondering if it is possible to use the information contained in plink bim/fam/bed files to know under which genes snps fall? For example, is there a tool, say an R package, that will allow me to do this or is it impossible(Do I need more information)? Is there a tool that uses snps' physical position(bim file) and then maps them to genes?

My ultimate goal is to somehow use the bim/fam/bed files that I have and come up with a snp gene mapping file.

I have spent quite a long time now looking for tools/ reading articles in order to find an answer but I have had no success. I am fairly new to the field of computational biology, and I would appreciate any help that I can get.

Answer 1

[Philipp Bayer]

I think that's possible -

You can use PLINK2's --recode vcf (possibly vcf-iid, vcf-fid) to convert the PLINK bim/fam/bed to a vcf. From there you can create a new database in SnpEff for your reference: http://snpeff.sourceforge.net/SnpEff_manual.html#databases You only have to do that if your genome isn't included in the available databases.

From there you can use SnpEff to annotate your SNPs with whether they're in genes, and whether they cause any changes there: http://snpeff.sourceforge.net/SnpEff_manual.html#run

[apilarmoreno4]

Thank you! I will check it out.