On the alternate allele frequency #429
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Hi Jinshanmu
Thanks for bringing this to our attention.
There is a metadata error in dataset ieu-a-1013. The effect allele columns are mislabelled. The effect allele (ea) is actually the non-effect allele (nea) and effect allele frequency (eaf) actually refers to the non-effect allele (nea).
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Subject: [MRCIEU/TwoSampleMR] On the alternate allele frequency (Discussion #429)
I have a question on the number of alternate allele frequency (AF) / effect allele frequency (EAF) in the IEU OpenGWAS. Take rs12562034 in the ieu-a-1013 data for example, it has AF = 0.895 for the alternate allele A. However, when querying PhenoScanner or GRCh37 Ensembl, the A allele has a frequency of 0.09 in the European population. Is there a confusion between alternate allele and reference allele in the data curation process?
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I have a question on the number of alternate allele frequency (AF) / effect allele frequency (EAF) in the IEU OpenGWAS. Take rs12562034 in the ieu-a-1013 data for example, it has AF = 0.895 for the alternate allele A. However, when querying PhenoScanner or GRCh37 Ensembl, the A allele has a frequency of 0.09 in the European population. Is there a confusion between alternate allele and reference allele in the data curation process?
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