Map snps to its genes
How to map snps in my ped file to their genes using plink?
I need to group these snps based on their belong genes.
such as x, y and z snps belong to gene w.
It's good idea to give some rows of data. Without it, I can only suggest reading this page:
The basic idea is:
- have chromosome and base position for the SNPs
- have a gene list with chromosome, start, end position, and gene names
- run the ./plink --gene-report command
You can convert the ped file to vcf using plink, input the vcf file to ANNOVAR and obtain the genes that the SNPs map to.
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