How to find LD matrix for a large group of SNPs (more than 6000 SNPs)
As the question shows, I want to calculate the LD matrix of 6000 + SNPs with only knowing the rsid of the SNPs.
I have checked that I can use Plink to do it if I have bfile or vcf file, but unfortunately I do not have.
If I use LDlink website I can calculate maximum 300 SNPs while 3000 SNPs with API by R coding.
Do I have option to calculate the LD matrix of 6000 + SNPs with rsid but without other information?
Thank you very much and look forward to your kind help.
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Phylicia •
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