Whats the format for PLINK .set file for epistasis analysis?
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15 months ago

I'm trying to run variant interaction analysis in PLINK with the following comman:

plink \
  --bfile plink \
  --pheno pheno \
  --epistasis \
  --set-test \
  --set list_of_variants \
  --out plink

But as a reslt have a following error: Error: Last token in --set file isn't 'END'.

The list_of_variants is a .set file which i though is just a list of rsIDs (in this case two lists separated with tab). Apparently, however, it is not the case. What the correct format for .set file in PLINK?

plink epistasis .set • 457 views
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