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Find data on linkage among a bunch of known SNPs

Hi,

I apologize if the question is too basic.

I am working on a bunch of known human SNPs, and I was wondering if there was any way to study if these SNPs are linked and might occur on the same haplotype in a non-random frequency. Is this type of study called Linkage Disequilibrium? How do I perform such a study, and am I missing data points?

Any help and/or pointers on this would really help me. Thank you in advance for your response.

--
Ram

linkage snp
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written by Ram Ram

1 answer

Did you read this How To Perform A Multilocus (Snp Genotype Data) Linkage Disequilibrium Analysis Using R?

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updated by Ram Ram • written by Sukhi Singh Sukhi Singh

Thank you, Sukhdeep. That is an amazing resource. Just wondering - I just have a bunch of known rs#, would I need to find the VCF files as well?

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written by Ram Ram

SNP identifier from dbSNP.

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written by Ram Ram

Sorry, I don't know about that.

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written by Sukhi Singh Sukhi Singh

It's OK, Sukhdeep. The link you gave me will help me get started on my search. Thank you so much for the pointer!

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written by Ram Ram

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