Opened 8 months ago

Closed 8 months ago

#1238 closed defect (fixed)

Convert variants annotations to TEXT type

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: Reggie v4.26.2
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

The annotation types are currently created with STRING type (see #1229 [5872]). The problem with this is that the STRING data type has a limit of 255 characters. If several variants are found in the same gene the value can be longer than this. For example, we got the following error message:

Error: String too long. The 'PTEN_Variants' mustn't be longer than 255 characters. 
The supplied value 'chr10:87864283:G>T,...' is 418 characters.

Unfortunately it is not possible to change the value type for annotation types. We need to remove all existing annotations and delete the existing annotation types before we can re-create annotation types and run the batch importer again.

  1. Export a file with the ID of all variant call raw bioassays. No other columns are needed. The Excel format can be used.
  2. Add headers to the exported file for each of the 21 variant annotation types:
    AKT1_Variants
    ARHGAP35_Variants
    ARID1A_Variants
    CBFB_Variants
    CDH1_Variants
    ERBB2_Variants
    ESR1_ResistanceVariants
    FOXA1_Variants
    GATA3_Variants
    KMT2C_Variants
    MAP3K1_Variants
    NFIC_Variants
    PIK3CA_Variants
    PLEC_Variants
    PTEN_Variants
    RNF213_Variants
    RUNX1_Variants
    SF3B1_Variants
    TBX3_Variants
    TP53_Variants
    TRPS1_Variants
    

Use the attachment:headers-for-import.txt file as template.

  1. Upload the file to BASE and run the Annotation importer plug-in. Make sure that Identification method=Internal ID, that all columns are mapped correctly and that the Remove existing option is enabled in the third step.
  2. When all annotations have been deleted it should be possible to delete the 21 annotation types as well.
  3. Also delete the Import variants from existing variant calls item list.
  4. Empty the trashcan so that the 21 annotation types and item list is properly removed.
  5. Update Reggie and run the Installation wizard.
  6. Run the Import variants for existing variant call raw bioassays.

Attachments (1)

headers-for-import.txt (326 bytes) - added by Nicklas Nordborg 8 months ago.
A tab-separated file with headers to use in the import step

Download all attachments as: .zip

Change History (4)

comment:1 Changed 8 months ago by Nicklas Nordborg

Description: modified (diff)

Changed 8 months ago by Nicklas Nordborg

Attachment: headers-for-import.txt added

A tab-separated file with headers to use in the import step

comment:2 Changed 8 months ago by Nicklas Nordborg

Description: modified (diff)

comment:3 Changed 8 months ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed

In 5912:

Fixes #1238: Convert variants annotations to TEXT type

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