Use LD statistics to find proxy SNP

Question

[sabir.saluja]

I am working with large VCF files to analyze a particular SNP. But the SNP was only sequenced for about 10% of the subjects in the VCF file. How can I use LD statistics from VCFTools to find a proxy SNP for the particular SNP I want to analyze?

Answer 1

[Veera]

You can find proxies for your snp using SNAP webtool from broad institute. Here's the link

[sabir.saluja]

This is working well. Thanks a lot for the help. What is the difference in the method used to find LD between VCFTools and the SNAP webtool?