PLINK meta-analysis - multiple parameters after '+'
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5.6 years ago
tarumuranen ▴ 10

Is it possible to do a PLINK (1.9) meta-analysis using .qassoc files as input?

The files look like:

CHR            SNP              BP    NMISS        BETA            SE             R2           T                P 
   21 rs4577363   14505577          25     0.3334     0.3214    0.04468    1.037       0.3104

From the documentation I understand that I should use parameters qt (to indicate that this is from linear association) and no-allele (to ignore that A1 is missing), but I cannot get the syntax correct. Currently I have:

plink --meta-analysis resultsfile1.qassoc resultsfile2.qassoc + qt no-allele --out meta_analysis_results

Can somebody help me, please?

To clarify, I get an error message:

Error: Invalid --meta-analysis parameter ' '.

I suppose this refers to the white-space between qt and no-allele.

snp plink • 931 views
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