Question: Map snps to its genes
2
gravatar for forever
3.7 years ago by
forever80
forever80 wrote:

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 • 1.5k views
ADD COMMENTlink modified 3.6 years ago by vakul.mohanty240 • written 3.7 years ago by forever80
0
gravatar for biocyberman
3.7 years ago by
biocyberman810
Denmark
biocyberman810 wrote:

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
ADD COMMENTlink written 3.7 years ago by biocyberman810
0
gravatar for vakul.mohanty
3.6 years ago by
vakul.mohanty240
United States
vakul.mohanty240 wrote:

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.

ADD COMMENTlink written 3.6 years ago by vakul.mohanty240
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