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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
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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)

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written by abascalfederico abascalfederico

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