--clump with multiple output

[Gloria Benoit]

Hi, 

I'm searching for more information about the behavior of --clump when multiple output are specified, ie plink --bfile mydata --clump mytest1.assoc,mytest2.assoc,mytest3.assoc.

If a SNP passes the p1 threshold in only one output, does it still register as an index snp, or does it have to pass p1 in every output?

Is there a doc somewhere that I have missed about this subject?

Thank you

[Christopher Chang]

- Only the best p-value is used for index-variant candidacy (and the file the p-value came from is reported in the 'F' column).

- For the later columns, when a variant appears in multiple files, it's counted separately each time (and in the SP2 column, the same variant can appear multiple times).

I will add this information to the online documentation.