Keeping Only Informative SNPs
Dear All I want to extract only unlinked snps only, how can do that? After the filter I have around 900 snps, among all the snps 480 snps are unlinked snps , I want to get a vcf files with only unlinked snps only. Any suggestion?
Kind Regards Safi
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safiq713 •
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How are you defining 'informative SNPs'?
Oh sorry only unlinked snps only
Ok, sounds like you want to LD-prune then? This post might help Plink: Understanding LD Clumping vs Pruning
as 4galaxy77 suggested, there are a million pre-written solutions to this. can just google this search query and find a software you like. ' if you have a more specific request, like I want to LD prune while also optimizing for this, that might be more appropriate for this forum