log-transformed P-values in the clump command

[Claudia Giambartolomei]

Hi, 

Some association softwares nowadays (Regenie) give only the -log10(P-value) column for GWAS results so I was wondering, 

is there a way to tell Plink or Plink2 that the to use the log-transformed P-values in the --clump command, and would the p1 and p2 threshold be also log transformed? 

Thank you,

Claudia 

[Chris Chang]

This feature should be available in plink2 within the next few days; I’ll post another reply here when the new build is ready.

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[Christopher Chang]

This feature is available in today's plink2 build: "--clump ... --clump-log10".  Note that plink2 --clump has a slightly different output file format than plink 1.x --clump.

You can either specify the p1/p2 thresholds the usual way (--clump-p1 / --clump-p2), or in -log10(p) form with --clump-log10-p1 / --clump-log10-p2.

[Christopher Chang]

Just a heads-up, you won't want to keep using that build since I broke --glm in it, oops.  (Though --clump should work fine.)  Build with unbroken --glm is now posted.