Question: Paper for Plink LD clumping 'greedy algorithm'
1
gravatar for Lou
2.0 years ago by
Lou10
Germany
Lou10 wrote:

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!

clumping ld plink greedy gwas • 1.0k views
ADD COMMENTlink modified 4 months ago by Biostar ♦♦ 20 • written 2.0 years ago by Lou10
1
gravatar for chrchang523
4 months ago by
chrchang5234.4k
United States
chrchang5234.4k wrote:

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.
ADD COMMENTlink modified 4 months ago by zx87546.2k • written 4 months ago by chrchang5234.4k
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