SKAT-O computing time

[Yi Yu]

Hi, 

I am trying to use SKAT-O in pseq0.09 for gene-based test for all genes in the genome on around 8K samples. It seems taking a lot of time to compute? I didn't see any output generated yet after 24hrs.  On the other hand, SKAT takes just several minutes for the same job. Just wondering if there is anything not right, as both SKAT and SKAT-O in PSEQ is not through permutation.  Below are the commands I used:

SKATO : >24hr, no output yet

pseq project assoc --tests skato --phenotype phen --mask loc.group=refseq > out.skato

SKAT : this runs fast

seq project assoc --phenotype phen --mask loc.group=refseq > out.skat

Thanks!

[cro...@gmail.com]

Hi Yi,

I was having the same issue (where SKAT-O was running very slow compared to other tests).  I was just wondering if you figured out a solution?

Thanks,
Carlos