Lea K.
Data Analyst
UKB Community team
Activity overview
Latest activity by Lea K.
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Lea K. created an article,
Integrating External Data Sources with UK Biobank on the RAP
The UK Biobank Research Analysis Platform (UKB-RAP) gives researchers restricted, cloud-based access to one of the world’s largest and most detailed health datasets. It includes information from ov...
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Lea K. commented,
Hi Thomas,Thanks for sharing your method, this is correct. One potential alternative could be to utilise the Swiss Army Knife in order to run a pre-defined script/function on the input data without...
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Lea K. commented,
Hi Shuangshuanag,You can access and manage files in your project by navigating through your folders using the DNAnexus tab in JupyterLab. This allows you to view and interact with your project file...
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Lea K. commented,
Hi Meghana,SAS is not available on the UKB-RAP, but we are considering supporting it in the future.Thank you for using the Community forum.
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Lea K. commented,
Hi Ian,That's the correct structure. However, please note that the base positions in the genotyping data are in GRCh37 coordinates so the start and end variant positions will be different. Hope thi...
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Lea K. commented,
Hi Jan,Thank you for using the Community forum. No, you do need UK Biobank RAP credentials to use the app.
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Lea K. commented,
Hi Ian,Thank you for reaching out. We are working on enhancing the documentation and tool for filtering SNPs in the genotyping data. If you want to filter the data based on the genomic positions t...
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Lea K. commented,
Hi Murad,Thank you for reaching out. You might find the xargs argument useful to execute jobs in parallel. For example:cat <list_of_files>.txt | xargs -I {} dx run <app> -iinput_file={} --destinati...
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Lea K. commented,
Hi Maria,Sorry for the delayed response. When trying to merge the diagnoses from field 41280, the order matches the order of the piped 41270 field. The data in the hesin_diag table follows a differ...
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Lea K. commented,
Hi Sai,You can use PLINK to extract genetic variants from WGS data. You may find the SNP extraction notebook useful, it extracts variants from the genotype data. You can do a similar analysis on th...
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