Data enquiries
UKB-RAP, Showcase and data baskets
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We highlighted a potential issue with allele frequencies for multi-allelic variants in the UKBB WGS 200k data.
- Former User of DNAx Community_58
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New Data Release on UKB-RAP: 200k WGS Phased Genomics Data, OMOP & Data Refreshes
- Brenton Pyle
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How to Access OMOP database of ukbiobank?
- Former User of DNAx Community_6
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Why there are so many mutations with a high percentage of unknown data in chromosome 6?
- Former User of DNAx Community_61
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Is there any dataset with only clinvar pathogenic variants information only?
- Former User of DNAx Community_6
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Questions/Error: ukb-rap-pheno-basic.ipynb
- Former User of DNAx Community_69
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I am trying to access accelerometry data. I would like to know how to use these datasets and are there any tutorials available for the analysis ?
- Former User of DNAx Community_6
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Many sample-level WGS gVCFs lack mitochondrial variant calls in UKB
- Former User of DNAx Community_7
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I'm trying to look for reports of a specific disease in a range of datasets. I used the cohort browser and then ran a Jupyter notebook with PySpark to get the data. ICD-10, -9, etc. works,but "Non-cancer illness code, self-reported" gives a Py4JJava error
- Former User of DNAx Community_20
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Why is HAIL SampleQC script stalling in JupyterLab?
- Former User of DNAx Community_82
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Downloading updated NMR metabolomic data
- Former User of DNAx Community_44
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Taking too long to update UKB dataset
- Former User of DNAx Community_10
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I am trying to generate a diet score and having hard time. Can someone help me with the analysis.
- Former User of DNAx Community_6
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ICD-10: L20 Atopic Dermatitis vs. Data Field 131720: Date L20 first reported
- Former User of DNAx Community_36
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I am trying to figure out how to subset the protein expression dataset to participants that were randomly selected. Is there a field that denotes whether or not a participant with proteomics data is randomly selected vs preselected by the consortium?
- Former User of DNAx Community_33
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Help avoiding memory issues with table exporter.
- Former User of DNAx Community_44
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Mapping ICD10 codes from field 41270 via PheWAS R package using createPhenotypes results in only ~1250 phenotypes. Does anyone know how to get ALL the phenotypes in the UKB - but particularly all related to mental disorders?
- Former User of DNAx Community_66
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How to download NMR metabolomics data?
- Former User of DNAx Community_44
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Will the bgenix index files be available for the WGS 200k interim, or do we have to create them?
- Former User of DNAx Community_58
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Does anybody else encounter random read errors when reading imputed genotypes ?
- Former User of DNAx Community_48
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How can we execute modified applets without creating duplicated data?
- Former User of DNAx Community_55
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Why do our forum passwords need to be reset every 3 months?
- Former User of DNAx Community_55
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Is it possible to access returned data on UKB RAP? I have identified the relevant details of the data I'm interested through the publication (return ID, etc.), though I am unable to find the data using Spark.
- Former User of DNAx Community_33
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Could you please offer the List of Field Names for All Proteins so that we can download all the proteomic data ?
- Former User of DNAx Community_43
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I have a question about the "Haplotypes" file (the 0.06TB one - BGEN and BGI). Does this file only contained pruned SNPs after eliminating those in high LD? I am unable to understand how the haplotypes are stored here. Please Help!
- Former User of DNAx Community_37
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Location for publicly available models and processed data
- Former User of DNAx Community_64
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How to improve the disk speed and data transfer speed in UKB RAP VMs
- Former User of DNAx Community_15
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Is there a way to skip outputs already generated in WDL?
- Permanently deleted user
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How could we merge exome data (GRch38) and genotype data (GRch37) to explore their LD?
- Former User of DNAx Community_99
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Hi, I recently noticed that some participants have been automatically removed from the UKB dataset when I updated the dataset. However, I have been working with the previous data, and I want to remove these participants from my datasets
- Former User of DNAx Community_84
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