Find data on linkage among a bunch of known SNPs

Question

[Ram]

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

Answer 1

[Sukhi Singh]

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

[Ram]

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?

[Sukhi Singh]

what is rs#

[Ram]

SNP identifier from dbSNP.

[Sukhi Singh]

Sorry, I don't know about that.

[Ram]

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