LD between CNVs and exterior SNPs
Hello everyone,
I have a few copy number variants (all multi-allelic) and trying to estimate LD between these CNVs and all SNPs across the genome (I am interested in LD between CNVs and "exterior" SNPs). In the past I have estimated LD between biallelic SNPs. I just converted my vcf file into 0,1,2 genotype matrix (0,1,2 are number of alt alleles), and simply calculated R2 by a very simple R-code. But in the current case (SNPs and multi allelic CNVS) I am confused how to proceed. Can anyone help me to get some ideas where to start? Any suggestion is appreciated ..
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I'm trying to perform a similar analysis. Did you get any answer ? did you try using PLINK ?