I previously reported that the SAMPLE IDs in the .bgen files provided as part of the GEL imputation release were incorrect and specific to the source project that created them. This appears to have been corrected. However, now the .bgi files appear to NOT have been regenerated following this change. Therefore, the byte positions in the index are now incorrect and cause issues when streaming with various tools (e.g., bgenix).
The .bgi files are indeed from the previous release. Could you share the sample command that you run and have issues with incorrect byte position for us to assess the impact?
Is there any update on this? I have been having the same issue running bgenix on the GEL imputed files and I am getting the same issue with the .bgi files. Works fine with the other imputed datasets, just the GEL imputed ones raise the error.
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Thanks for reporting this, @Eugene Gardner?. We will check into it.
@UK Biobank DA Team?
The .bgi files are indeed from the previous release. Could you share the sample command that you run and have issues with incorrect byte position for us to assess the impact?
Hello Chai,
I actually directly query the bgen files with custom python code, but I would imagine if you run something like:
bgenix -g <.bgen> -incl-rsids <some rsid from that chromosome>
It should error out, but I cannot confirm.
Thank you, Eugene. I confirm that bgenix tool would not work with this example. I normally use sqlite3 and it was okay, so I didn't notice.
I have informed both internal team & UKB, and we will discuss our approach to fix this. Thanks again for reporting this.
Hi there,
Is there any update on this? I have been having the same issue running bgenix on the GEL imputed files and I am getting the same issue with the .bgi files. Works fine with the other imputed datasets, just the GEL imputed ones raise the error.
Did you see the “fix” here?
How to resolve REGENIE errors with GEL and TOPmed BGEN indices
Thanks for the suggestion Richard. For future reference I'm providing a link to the article you mentioned: https://community.ukbiobank.ac.uk/hc/en-gb/community/posts/17179207789853-How-to-resolve-REGENIE-errors-with-GEL-and-TOPmed-BGEN-indices
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