WGS 500k PLINK and BGEN
Hello,
I am aware of the documentation that states that PLINK and BGEN files will be released at some point in 2024 for the WGS data. Does anyone know if this will be occurring some time soon or is this towards the end of 2024?
Thanks,
Andrew
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4 comments
There is a fairly strong expectation that at least one of them will be available at the next update, which is expected to be some time in Summer 2024. However, the date and the content are still not confirmed. When they are confirmed, they should be on the Future Timelines page, https://www.ukbiobank.ac.uk/enable-your-research/about-our-data/future-data-release-timelines
Hi Andrew, FYI, I'm afraid this is looking more like late-2024, though there is still a small possibility it might be early autumn. The recent announcement to go RAP-only has altered the priorities somewhat.
In that case, would you be so kind and provide a comprehensive guide on how to efficiently convert the existing genomic data to bgen and PLINK files please?
There is some documentation on how transform VCF to PLINK1.9 and BGEN (https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/whole-exome-sequencing-oqfe-protocol/protocol-for-processing-ukb-whole-exome-sequencing-data-sets). This was written before PLINK2 which is more compressed than PLINK1.9.
It may be better to run these as a series of apps or as a WDL. UK Biobank will be releasing information on a WDL that converts VCF to PLINK and BGEN through the github page, in the future. https://github.com/UK-Biobank
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