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.