Open kw8 opened 3 months ago
Hi Klaudia,
Could you include the REGENIE log from a run where you are seeing discrepancies?
Thanks, Joelle
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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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
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
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
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