Keeping Only Informative SNPs

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2.3 years ago

safiq713 ▴ 10

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

Extrcation NGS SNPs • 988 views

ADD COMMENT • link updated 2.3 years ago by LauferVA 4.2k • written 2.3 years ago by safiq713 ▴ 10

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How are you defining 'informative SNPs'?

ADD REPLY • link 2.3 years ago by 4galaxy77 2.8k

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Oh sorry only unlinked snps only

ADD REPLY • link 2.3 years ago by safiq713 ▴ 10

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Ok, sounds like you want to LD-prune then? This post might help Plink: Understanding LD Clumping vs Pruning

ADD REPLY • link 2.3 years ago by 4galaxy77 2.8k

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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

ADD REPLY • link 2.3 years ago by LauferVA 4.2k

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