What's the difference between Exome sequences_Alternative exome processing and Exome sequences in the Bulk data? Is there any document where we can read about this?
@Chai Fungtammasan? thanks for pointing out these resources. However in the showcase there's not explanation on where this data comes from? or if they include the number of samples in the final release or less? There's really no documentation at all for the DRAGEN and gnomAD versions. Can you point to more comprehensive documentation please?
We didn't receive them from UKB. I recommend that it's best for you to send this inquiry directly to UKB data access team. We have let them know, but I think they could prioritize it if community members are interested in using it.
For gnomAD, there is a file describing process in /Bulk/Exome sequences_Alternative exome processing/Exome variant call files (gnomAD) (VCFs)/helper_files/
I would start from that while waiting for more documentation from UKB. You could check on the header of vcf file too if they have any info you need.
Comments
4 comments
The main (Exome sequences) is OQFE while alternative are either DRAGEN or gnomAD. You can see more documentation in Showcase.
https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=171
https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=172
For OQFE, we maintain very detailed documentation on data processing here.
https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/whole-exome-sequencing-oqfe-protocol
@Chai Fungtammasan? thanks for pointing out these resources. However in the showcase there's not explanation on where this data comes from? or if they include the number of samples in the final release or less? There's really no documentation at all for the DRAGEN and gnomAD versions. Can you point to more comprehensive documentation please?
We didn't receive them from UKB. I recommend that it's best for you to send this inquiry directly to UKB data access team. We have let them know, but I think they could prioritize it if community members are interested in using it.
For gnomAD, there is a file describing process in /Bulk/Exome sequences_Alternative exome processing/Exome variant call files (gnomAD) (VCFs)/helper_files/
I would start from that while waiting for more documentation from UKB. You could check on the header of vcf file too if they have any info you need.
Thanks, I will contact UKB directly.
Please sign in to leave a comment.