Error in run_eggla_gwas when use_info=TRUE about eggla HOT 8 CLOSED

I hardcoded the imputation quality field in INFO as "INFO" while it could also be "R2".
I'll release a patch today.

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Ok, let me know if there is still an issue or if it goes smoothly, and in that case I'll release v0.17.4..

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Will do, with use_info=TRUE it took about 2,5 days to finish.

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This should be fixed now, can you try to install the development version?

remotes::install_github("mcanouil/eggla")

PS: do not forget to provide the proper information for the imputation quality metrics by changing the default value for info_type, i.e., info_type = "IMPUTE2 info score via 'bcftools +impute-info'", in your case it's something about "R2".

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Thanks, got the 0.17.4 and running the analysis now.

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I'll keep the issue open until you can confirmed it is fixed then.

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This worked! I quickly looked at the results, seems like everything else is OK I just need to add CALL_RATE.

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Great! I'll start the release process for v0.17.4.

I don't think the CALL_RATE is really needed though.
In theory, your data have been QCed, this implies a call rate threshold, thus the column will be between the threshold and one, which makes it not really useful for any postprocessing step.

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