Prune SNPs in LD with a list of SNPs

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5.5 years ago

aritra90 ▴ 70

Hi,

I have a list of SNPs. I want to find the SNPs in a genotype (Plink format) data set, which are in LD (> 0.2) with the list of SNPs. Any help on how to achieve this is appreciated.

Thanks.

SNP plink LD • 2.8k views

ADD COMMENT • link 5.5 years ago by aritra90 ▴ 70

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What have you tried? The plink online manuals are very extensive.

ADD REPLY • link 5.5 years ago by zx8754 11k

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I couldn't figure out the right command to enter a SNP list and a genotype file and obtain another snp list which are in high LD. For now I've been using indep-pairwise to remove the SNPs in high LD beforehand and then do downstream analyses. However, I wanted to remove SNPs which are in LD with a particular subset of SNPs (provided in a file such as what --extract/--exclude takes in as input)

ADD REPLY • link 5.5 years ago by aritra90 ▴ 70

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Not sure but you may try the --ld-snp-list flag, which accepts a file-listing of input SNPs for the purpose of identifying LD.

ADD REPLY • link 5.5 years ago by Kevin Blighe 87k

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