Whats the format for PLINK .set file for epistasis analysis?

Question

[optimistsso4co3]

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?

Answer 1

[chrchang523]

See https://www.cog-genomics.org/plink/1.9/formats#set .