PLINK/SEQ SKAT gives different p-values depending on number of tests run

Question

[p0078005]

We are using PSEQ to analyse rare variants at a gene-based level. I like the interface and the output from PSEQ but have noticed that if I run SKAT alone, I get a different p-value from if I run SKAT and (for example) C-alpha in the same line.

The input files are exactly the same, it is just the number of tests run that differ. Can anyone tell me if PSEQ uses a project-wide p-value adjustment by default (this is the only explanation I can think of to explain this).

Thanks DIanne

[WouterDeCoster]

As far as I know SKAT will return a different p-value every time you run it, regardless of running other tests. But that's the case if you just run SKAT in R. Not sure about PSEQ.