Opened 6 months ago

Closed 4 months ago

#1353 closed enhancement (fixed)

Search functionality for all genotypes on the OncoArray-500K

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.35
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

The implementation that started in #1346 should be extended to make it possible to implement search functionality in the Variant search extension.

To make this possible we need to make VCF files with all 500K variants that are on the OncoArray? SNP. We already have a procedure for this with the VCF for the QC so this should not be major problem. Depending on how the search is implemented we may need to make some changes.

Change History (4)

comment:1 Changed 4 months ago by Nicklas Nordborg

In 6538:

References #1353: Search functionality for all genotypes on the OncoArray?-500K

Added a raw data type for the OncoArray500K data. The intention is to create child raw bioassay item from the GenotypeCall derived bioassays and attach the full VCF file to the new raw bioassays.

comment:2 Changed 4 months ago by Nicklas Nordborg

In 6542:

References #1353: Search functionality for all genotypes on the OncoArray?-500K

Added a file type for VCF files that are used to define an array design.

comment:3 Changed 4 months ago by Nicklas Nordborg

In 6557:

References #1353: Search functionality for all genotypes on the OncoArray?-500K

Added some more annotation types for the OncoArray raw bioassays:

  • GenoTypeCount
  • GenoTypeREF_PCT
  • GenoTypeHET_PCT
  • GenoTypeALT_PCT

comment:4 Changed 4 months ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed
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