Merge OncoArray items with GenotypeCall item

[Nicklas Nordborg]

The OncoArray item type is logically the same as the GenotypeCall item type. They are created at the same time as a result of analyzing the !OncoArray500K chips. The reason for having two item types to begin with was to enable the Variant search extension to index the genotypes and it only worked with raw bioassay items to begin with. Since we moved all raw bioassay items to derived bioassays in Reggie 5.0 and the Variant search now works with derived bioassays it should be possible to merge the two item types to a single one.

This should be easy to do manually by copying some information with batch importers:

• File: genotypes_all.vcf.gz
• Annotations:
  • GenoTypeALT_PCT
  • GenoTypeHET_PCT
  • GenoTypeREF_PCT
  • GenotypeCount

Note that the genotypes_all.vcf.gz also need to be moved on the file server from the ../d.gt/v directory up one level. The same applies to the file item on lorry and it also need to update the URL so that it points to the new location.

The 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.

The annotations and VCF file is easy to copy by hand:

1. Display derived bioassays with subtype OncoArray.
2. Display the following columns:
   • Parent bioassays
   • VCF
   • GenotypeCount
   • GenoTypeALT_PCT
   • GenoTypeHET_PCT
   • GenoTypeREF_PCT
3. Export all (1995) to an Excel file
4. Change the table to only display bioassays with subtype GenotypeCall
5. Import the VCF file with the Derived bioassay importer:
   • Use Update mode
   • Use the 'Parent bioassays' column as the identifier column
   • Select the 'VCF' column as 'File' and enter 'VCF' in the File type mapping.
6. Import the annotations. Use the 'Parent bioassays' column as the identifier column.

[Nicklas Nordborg]

In 7781:

References #1601: Merge OncoArray items with GenotypeCall item

Add VCF as file type to GenotypeCall.
Add OncoArray annotations to GenotypeCall.

[Nicklas Nordborg]

In 7782:

References #1601: Merge OncoArray items with GenotypeCall item

Deprecated the OncoArray subtype.

[Nicklas Nordborg]

In 7783:

References #1601: Merge OncoArray items with GenotypeCall item

Updated Case summary.

[Nicklas Nordborg]

In 7785:

References #1601: Merge OncoArray items with GenotypeCall item

Changed the release exporter so that it export GenotypeCall items instead of OncoArray items.