Kristen

I second this suggestion.Plink is one of the most widely used genetics tools out there, and Plink's .bed format is widely supported by other genetics tools as well. Only making the data available i...

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• 14 August 2025 20:25
• 3 votes

Caveat to the above: When I say that Plink or most analysis tools will still produce correct allele frequencies, effect estimates, etc. I mean tools that use one data source for the whole process. ...

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• Edited 15 August 2025 04:20
• 2 votes

Here are results to confirm what Ahmet reported, the DRAGEN .bgen files are ref-last.Using the following test SNPs on chromosome 21, I compared different versions of the genotype data:rsid ...

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• Edited 15 August 2025 04:18
• 2 votes

There is a plink version of the 500k WGS data available now in pgen format.  If it makes sense, maybe migrate the analyses from the imputed data to the WGS plink datasets. Good suggestion, but thos...

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• 25 August 2025 17:49
• 0 votes

It's still there for me: /Bulk/Genotype Results/Genotype calls/ukb_rel.datHere are some things to check if you can't see it: Make sure you have the array genotyping data dispensed to your project. ...

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• Edited 14 August 2025 20:45
• 1 vote