FOCUS stalls on chromosome 6 about focus

[gg-n]

Hi

Thank you for making this great tool available!

@m-wilke, I have the same issue (using a p-threshold of 5e-6), it has been stuck at 6:30798168 - 6:31570931 for over 24h. May I ask if you have since managed to figure out the reason or find a solution? Any tips would be extremely helpful and appreciated.

Many thanks
GG

[m-wilke]

Hi @gg-n,

What I have done is I have removed the MHC/HLA region (the base pairs) from my GWAS summary statistic file and then re-ran FOCUS using the new summary statistics file. It seems as though the HLA region corresponds to where FOCUS is getting stuck.

I still have not solved my issue with chromosome 1 but hopefully that helps for chromosome 6!

MacKenzie

[gg-n]

Hi @m-wilke,

Thanks very much for the useful tip. I have tried this now (as the MHC/HLA region is not my main target) and it has reduced the running time to 3h for chr6! Unfortunately I can't be much help with the chr1 issue, but hopefully others reading this thread might have some suggestions.

Many thanks
GG