Comments (4)
chrchang
commented on August 17, 2024
I was unable to reproduce this problem on my Mac, so I've added some debug logging to the 20 February development build. Can you try reproducing the bug with that build and the --debug flag on, and send me the .log file (you can send to wdist [at] cog-genomics [dot] org)?
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kpalin
commented on August 17, 2024
It was user error. My bad. Sorry.
The FID and IID values were slightly wrong in the pheno file so that's why it didn't work. It might be worth outputting a statistics of phenotypes with and without matching genotypes.
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kpalin
commented on August 17, 2024
My bad but not the issue I thought. All of the controls were missing gender information and those were excluded from association analysis without a warning "--allow-no-sex" got them back.
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chrchang
commented on August 17, 2024
I actually received another report of a user being tripped up by this today, so I will add a warning for this tomorrow.
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Related Issues (20)
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