Convert variants annotations to TEXT type
|Reported by:||Nicklas Nordborg||Owned by:||Nicklas Nordborg|
Description (last modified by )
The annotation types are currently created with STRING type (see #1229 ). 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.
- Export a file with the ID of all variant call raw bioassays. No other columns are needed. The Excel format can be used.
- 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
- 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.
- When all annotations have been deleted it should be possible to delete the 21 annotation types as well.
- Also delete the Import variants from existing variant calls item list.
- Empty the trashcan so that the 21 annotation types and item list is properly removed.
- Update Reggie and run the Installation wizard.
- Run the Import variants for existing variant call raw bioassays.