Map snps to its genes

Question

[forever]

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.

Regards

Answer 1

[biocyberman]

It's good idea to give some rows of data. Without it, I can only suggest reading this page:

http://pngu.mgh.harvard.edu/~purcell/plink/grep.shtml

The basic idea is:

1. have chromosome and base position for the SNPs
2. have a gene list with chromosome, start, end position, and gene names
3. run the ./plink --gene-report command

Answer 2

[vakul.mohanty]

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.