This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to retrieve corresponding genes from a list of snps in preferably Plink...if possible

I'm going to attempt to ask the same question in a different way. Is there a way I can map genes to a list of snps in Plink so that the outcome contains both the snp and its corresponding gene on the same row? I have .snplist file from Plink that I plan to use as the input. The resulting output should at least look like this:

rs1234 Gene1234
rs4567 Gene4567
rs7892 Gene7892

Any assistance will be greatly appreciated. Other suggestions outside of Plink will be appreciated as well.

plink
• 1,999 views • link
updated by Ram Ram • written by Avoks • Avoks

I would make a bed or vcf file for those snps and then calculate the intersection with a bed of gene coordinates (using bedtools)

• 0 views • link
written by abascalfederico abascalfederico

0 answers

No answers yet.

Log in to answer this question.

More posts like this