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Use LD statistics to find proxy SNP

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?

snp ld vcf
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updated by Biostar Biostar • written by sabir.saluja • sabir.saluja

1 answer

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

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written by Veera Veera

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?

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written by sabir.saluja • sabir.saluja

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