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Paper for Plink LD clumping 'greedy algorithm'

Hello,

I am having some trouble finding the orginal paper that decribes the greedy algorithm used in Plink's LD clumping procedure. If someone could point me in the right direction or briefly explain how overlaps between clumps are dealt with so that no SNP can belong to more than one clump that would be wonderful.

Thanks!

plink gwas ld clumping greedy
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updated by Biostar Biostar • written by Lou • Lou

1 answer

This isn't explicitly described in a paper, but there are some details in the plink 1.9 documentation at https://www.cog-genomics.org/plink/1.9/postproc#clump .

Specifically, the core of the greedy algorithm is described in the first bullet:

  • Clumps are formed around central 'index variants' which, by default, must have p-value no larger than 0.0001; change this threshold with --clump-p1. Index variants are chosen greedily starting with the lowest p-value. Variants which meet the --clump-p1 threshold, but have already been assigned to another clump, do not start their own clumps unless --clump-best was specified.
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updated by zx8754 zx8754 • written by chrchang523 chrchang523

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