How to retrieve corresponding genes from a list of snps in preferably Plink...if possible
0
3
Entering edit mode
8.2 years ago
Avoks ▴ 40

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 • 1.6k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2475 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6