Tips on how to convert genetic data from BGEN to another format?

Analyzing and Reusing Data
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Hi,

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)?

Thanks!

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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.

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Hi Mei-Yu,

We recommend that QCTOOL is used for converting among formats: link.

A few other items I’d point out:

  1. The Annotated Data Dictionary has an entry (‘Genetic’) which includes information on this data.
  2. There is also the newly released QC info (this also includes platform annotations)
  3. Here is another thread talking about working with these data.

Hope this helps, looking forward to hearing more about the work you’re doing!

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Hi Josh,

Thank you so much for sharing useful information that is a big help!

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