Question

Which software can prune 5 Million SNPs?

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Weiqiong • 0

@3e09f576

Last seen 13 months ago

United States

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.

LinkageDisequilibrium SNP gwas GWASdata ldblock • 767 views

ADD COMMENT • link 14 months ago • updated 13 months ago Weiqiong • 0

score 0 · Answer 1 · 2023-03-14

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 3 hours ago

United States

You could use SNPRelate.

ADD COMMENT • link 13 months ago James W. MacDonald 65k

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Assuming of course that you have more than just the positions. I assume you have actual data?

ADD REPLY • link 13 months ago James W. MacDonald 65k

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Yes. I have a huge actual dataset to deal with.

ADD REPLY • link 13 months ago Weiqiong • 0

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Thanks a lot. I will try it.

ADD REPLY • link 13 months ago Weiqiong • 0