We highlighted a potential issue with allele frequencies for multi-allelic variants in the UKBB WGS 200k data.

Former User of DNAx Community_58
We are interested in running association analysis with plink using the bgen files for UKBB WGS 200k. Could you confirm this issue, and does it make sense to create a "blacklist" of multiallelic variants in order to exclude them before conducting association tests with plink? Thanks!

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    Chai Fungtammasan DNAnexus Team

    Are you asking if the file containing multiple allele or are you implying that there is an issue with data?

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