Question: Tools For Calculating Pairwise R2 Ld Estimator Between Snps In Different Scaffolds
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gravatar for bmartinez
6.0 years ago by
bmartinez0
bmartinez0 wrote:

Hi all,

I am estimating the pairwise r^2 LD estimator between SNPs I have selected for a SNP chip. I would like to estimate this r^2 between any pair of SNPs selected despite their location in different scaffolds. (I have several genotypes for each marker). I am using vcftools to do so. Otherwise I get only the r2 estimates between SNPs within the same scaffold. Does anyone know how to do it between any pair of SNPs, regardless of the situation?

Thanks a lot in advance, best!

vcftools ld • 2.8k views
ADD COMMENTlink modified 6.0 years ago by zhengxwen0 • written 6.0 years ago by bmartinez0
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gravatar for zhengxwen
6.0 years ago by
zhengxwen0
zhengxwen0 wrote:

You could try the function 'snpgdsLDMat' in the R package SNPRelate.

ADD COMMENTlink written 6.0 years ago by zhengxwen0
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