Literally, field 23158 final exome release is ~470k , see https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=23158 which says Participants 469,602. On the RAP it is in folder Bulk > Exome sequences > Population level exome OQFE variants, PLINK format - Final exome release . The exome regions for most of the UKB participants were sequenced a few years ago.
In November 2023, UKB released whole genome sequencing for almost all the 500k UKB participants. Literally, there are results available for ~490k participants, as some samples were unusable or failed qc checks, but it is called “the 500k wgs release”, and the folders have [500k release] as part of the name. See eg field 23372 in RAP folder Bulk > GATK and GraphTyper WGS > Whole genome GATK CRAM files and indices [500k release] and field 24048 in RAP folder Bulk > DRAGEN WGS > Whole genome CRAM files (DRAGEN) [500k release] . See also Showcase category 180 https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=180 .
For future reference, if you start a new thread for a new question, people are more likely to see your post, rather than adding to an old thread. This particularly applies to the threads that have been imported from the old dnanexus forum, as they no longer send updates to the previous posters in the thread.
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It's in the name of the file or in the header of pVCF depending on data type. This will be covered in Overview webinar next week. https://hello.dnanexus.com/uk-biobank-research-analysis-platform-overview
If the data is in PLINK or BGEN format you can use PLINK2 to extract samples by using --keep parameter .
For example, if you are using final exome release (field ID 23158)
plink2 --bfile ukb23158_c22_b0_v1 --keep eids_list.txt --out ukb23158_c22_b0_v1_filtered
Here, eids_list.txt contains one EID per line.
You need to do this for each chromosome.
final exome release (field ID 23158)，is this 500k release?
Literally, field 23158 final exome release is ~470k , see https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=23158 which says Participants 469,602. On the RAP it is in folder Bulk > Exome sequences > Population level exome OQFE variants, PLINK format - Final exome release . The exome regions for most of the UKB participants were sequenced a few years ago.
In November 2023, UKB released whole genome sequencing for almost all the 500k UKB participants. Literally, there are results available for ~490k participants, as some samples were unusable or failed qc checks, but it is called “the 500k wgs release”, and the folders have [500k release] as part of the name. See eg field 23372 in RAP folder Bulk > GATK and GraphTyper WGS > Whole genome GATK CRAM files and indices [500k release] and field 24048 in RAP folder Bulk > DRAGEN WGS > Whole genome CRAM files (DRAGEN) [500k release] . See also Showcase category 180 https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=180 .
For future reference, if you start a new thread for a new question, people are more likely to see your post, rather than adding to an old thread. This particularly applies to the threads that have been imported from the old dnanexus forum, as they no longer send updates to the previous posters in the thread.
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