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rgcgithub / regenie

regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.
https://rgcgithub.github.io/regenie
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SKAT problems #539

Open kw8 opened 3 months ago

kw8 commented 3 months ago

Hi, We observed that when we use the following AAF bins for SKAT and SKAT-O and a maximum AAF threshold of 0.001, we sometimes get a SKAT/SKAT-O output for 0.01, and in only those cases we don't get an output for 0.001. --aaf-bins 0.01,0.001 --vc-tests skat,skato --vc-maxAAF 0.001 Is this a bug or do we misinterpret the results? Many thanks, Klaudia

joellembatchou commented 3 months ago

Hi Klaudia,

Could you include the REGENIE log from a run where you are seeing discrepancies?

Thanks, Joelle

kw8 commented 3 months ago

Hi Joelle,

Many thanks for replying so quickly. I attach the log files and the REGENIE output for the MT4 gene which shows this behaviour.

Many thanks, Klaudia

Klaudia Walter, PhD Martin Lab, Human Genetics Wellcome Sanger Institute Hinxton CB10 1HH

From: Joelle Mbatchou @.> Reply to: rgcgithub/regenie @.> Date: Tuesday 23 July 2024 at 16:27 To: rgcgithub/regenie @.> Cc: Klaudia Walter @.>, Author @.***> Subject: Re: [rgcgithub/regenie] SKAT problems (Issue #539) [EXT]

Hi Klaudia,

Could you include the REGENIE log from a run where you are seeing discrepancies?

Thanks, Joelle

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joellembatchou commented 2 weeks ago

Hi Klaudia,

The log did not get attached here; the SKAT/SKATO results should only be shown for the mask AAF threshold specified. Perhaps for that MT4 gene you could include a snippet of the sumstats file showing the ALT/MODEL/LOG10P columns?

Cheers, Joelle

kw8 commented 2 weeks ago

Hi Joelle, Apologies that the email attachments did not work. I try to attach them again here. Many thanks, Klaudia

2023_08_09_AFP__fit_out.log 2023_08_09_AFP__GNH_genetests.log.gz 2023_08_09_AFP__GNH_singlevariantExWAS.log MT4.regenie.out.txt

joellembatchou commented 2 weeks ago

Hi Klaudia,

Thank you for attaching the files. I tried replicating your issue with the same REGENIE version but was unsuccessful. Could you re-run with the latest REGENIE version for just MT4 (i.e. using --extract-setlist MT4), specify --debug and attach the resulting output (logs & sumstats files)? You could just do it for one of the traits (e.g. AFP.mean).

Thanks, Joelle