Hello, When looking at a specific variant in a cohort in the Genomics tab, is it possible have access to IDs of the patients having this specific variant ? Thank you !

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  Ondrej Klempir DNAnexus Team

  • 21 September 2022 08:37

  This worked for me:

   

  

  1. Specified a genotype filter, i.e. rsid.
  2. Clicked on Data Preview tab.
  3. Inspected the filtered Participant IDs (samples / eids).
  4. Could export sample ids directly to csv OR
  5. Saved results to a new filtered cohort in order to process this further in JupyterLab or with TableExporter.
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  Former User of DNAx Community_74

  • 21 September 2022 13:55

  You answered my question, thanks a lot !

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  Ashwin Lakshman Koppayi

  • 14 January 2025 18:52

  Hi,

  Is there a command line tool to do this. Basically, i have to get participant id for 66 variants and its time consuming to do it this way. 

  Please suggest!

  Thank you!

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  Rachael W UKB Community team Data Analyst

  • 17 January 2025 01:38

  Hi Ashwin,

  I don't think there is a command line way to interact with the cohort browser's genomic search.  (If anybody knows a way, please let us know below.)

  There must be command line ways to interrogate the underlying WES data files, as some previous studies have used data of thousands of variants.  Please have a look at the tools in the Swiss Army Knife, which can be found in the Tools Library

  

   

  

   

  If the variants you are interested in are simple SNPs, and if they are covered by the Genotype Calls, you could try using UKB notebook https://github.com/UK-Biobank/SNP-filtering .  There is a related forum thread about using this notebook at https://community.ukbiobank.ac.uk/hc/en-gb/community/posts/18669657313437-How-do-I-extract-allele-combinations-at-specific-SNPs-using-Jupyterlab .

  For more information about the different kinds of genetic data in the UKB, see Showcase Category 100314  and sub-categories.

   

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