Entering edit mode
8.8 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.
I would make a bed or vcf file for those snps and then calculate the intersection with a bed of gene coordinates (using bedtools)