Changes between Version 1 and Version 3 of Ticket #1601


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Timestamp:
Jun 20, 2024, 9:58:33 AM (5 months ago)
Author:
Nicklas Nordborg
Comment:

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  • Ticket #1601 – Description

    v1 v3  
    1313
    1414The !OncoArray items currently also have files and annotations that are related to the imputation analysis. They should not be moved to the !GenotypeCall items. Instead we should adjust the imputation analysis so that they have their own derived bioassays (eg. !ImputedGenotypes). See other ticket #1602.
     15
     16The annotations and VCF file is easy to copy by hand:
     17
     18 1. Display derived bioassays with subtype `OncoArray`.
     19 2. Display the following columns:
     20   - Parent bioassays
     21   - VCF
     22   - !GenotypeCount
     23   - GenoTypeALT_PCT
     24   - GenoTypeHET_PCT   
     25   - GenoTypeREF_PCT   
     26 3. Export all (1995) to an Excel file
     27 4. Change the table to only display bioassays with subtype `GenotypeCall`
     28 5. Import the VCF file with the Derived bioassay importer:
     29   - Use Update mode
     30   - Use the 'Parent bioassays' column as the identifier column
     31   - Select the 'VCF' column as 'File' and enter 'VCF' in the File type mapping.
     32 6. Import the annotations. Use the 'Parent bioassays' column as the identifier column.