LD between distinct set of SNPs and other other SNP's in the gnome - Plants
I am looking for a way to find a relationship between a set of 10 SNP's and all other SNPs in the genome. I want to know if there is any correlation between these SNP's being 'CATGCATGAC' and other SNP's or sets of SNP's in the genome. I have a VCF file containing thousands of plant lines and have been trying to use PLINK to find any correlation but am struggling.
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ryanzapotocny •
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