Map snps to its genes
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6.2 years ago
forever ▴ 80

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

SNP gene • 2.0k views
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6.2 years ago
biocyberman ▴ 840

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
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6.1 years ago
vakul.mohanty ▴ 260

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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