I’ve recently download the Fox Insight genetic data and realized it is in BGEN format. Does anyone have tips on how best to convert it to another format such as PLINK of VCF, and anything I should be particularly wary of when doing so (e.g., challenges you’ve faced when attempting to do this)?
Hi, I’m working on the Fox Insight genetic data. Have you found the best way to convert BGEN files to PLINK format? I encountered challenges in that there are multiallelic variants in BGEN, and PLINK does not support the import of data with multiallelic variants.