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I have a list of more than 5 million SNPs. I have each SNP's chromosome, position and rsID. Is there any software can be used to perform LD based pruning on so many SNPs? I want to prune, but not clump because there are no statistics to rank them.
Besides, those 5 million SNPs is a subset of 14 million SNPs, which do not necessarily have rsIDs. It will be better if I can prune all 14 million SNPs without using their rsIDs.
I appreciate any hints. Thanks a lot.
Assuming of course that you have more than just the positions. I assume you have actual data?
Yes. I have a huge actual dataset to deal with.
Thanks a lot. I will try it.