Question: Paper for Plink LD clumping 'greedy algorithm'
gravatar for Lou
20 months ago by
Lou10 wrote:


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.


clumping ld plink greedy gwas • 833 views
ADD COMMENTlink modified 11 days ago by Biostar ♦♦ 20 • written 20 months ago by Lou10
gravatar for chrchang523
10 days ago by
United States
chrchang5233.9k wrote:

This isn't explicitly described in a paper, but there are some details in the plink 1.9 documentation at .

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.
ADD COMMENTlink modified 10 days ago by zx87545.0k • written 10 days ago by chrchang5233.9k
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