This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to calculate LD values of SNP based on chromosomal positions and their call rate?

Hi to all Good Afternoon

I have file containing SNPs (affy 44k chip) with their call rate and chromosomal positions with me and these belongs to rice crop. Now how can i calculate LD values (r2) for these SNPs, my basic objective is to select tag SNPs based on LD for genotyping work. any help with any R packages or own functions in this regard will be highly appreciated Thanks in Advance

regards

snp snp r
• 2,455 views • link
written by blacktomato27 blacktomato27

To calculate LD you need a set comprising many genotypes (similar hapmap or 1kG, see also 1000 Genomes Ld Calculation ) from possibly many populations, do you have that? A quick google search did not reveal a genome wide public resource like that, but some older papers studying a selection of genotypes.

• 0 views • link
written by Michael Dondrup Michael Dondrup

0 answers

No answers yet.

Log in to answer this question.

More posts like this