In some rare occasion, p-values are delivered as log-transformed, and in those cases the following check causes all variants to be dropped:
https://github.com/FINNGEN/META_ANALYSIS/blob/9faf18a4f1762326bb92e724c869eb0641f5f8c1/wdl/munge.wdl#L95
P-values as such are only used when generating QQplots in the munging workflow, so it might be worth considering whether this check should be changed, or removed. Valid beta, SE, and AF values are much more important in the analysis.
In some rare occasion, p-values are delivered as log-transformed, and in those cases the following check causes all variants to be dropped: https://github.com/FINNGEN/META_ANALYSIS/blob/9faf18a4f1762326bb92e724c869eb0641f5f8c1/wdl/munge.wdl#L95 P-values as such are only used when generating QQplots in the munging workflow, so it might be worth considering whether this check should be changed, or removed. Valid beta, SE, and AF values are much more important in the analysis.