Opened 13 months ago

Closed 12 months ago

Last modified 12 months ago

#1549 closed enhancement (fixed)

Add support for viewing variant details from the WGS variant calling

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Variant Search v1.10
Component: net.sf.basedb.varsearch Keywords:
Cc:

Description

We would like to enabled the "More information..." link in Reggie that opens a popup with information about the variant and also include a tab with all information from the VCF file.

We can't do that now since it causes a NullPointerException. This is easy to get rid of, but the information that is displayed need some modifications.

  • It is not aware of having multiple samples in the same VCF file. The display takes information from the normal.
  • There are fields related to information that is only available in the RNAseq variant calling

Change History (8)

comment:1 by Nicklas Nordborg, 13 months ago

In 7474:

References #1549: Add support for viewing variant details from the WGS variant calling

The NullPointerException has been fixed.

comment:2 by Nicklas Nordborg, 13 months ago

In 7475:

References #1549: Add support for viewing variant details from the WGS variant calling

Hide RNAseq related information if the variant is from WGS.

comment:3 by Nicklas Nordborg, 13 months ago

In 7476:

References #1549: Add support for viewing variant details from the WGS variant calling

The VCF parser can now handle multiple samples, and the popup that display information can now display FORMAT information for all samples on the "Summary" tab (the "All" tab has not been updated yet).

comment:4 by Nicklas Nordborg, 13 months ago

In 7477:

References #1549: Add support for viewing variant details from the WGS variant calling

Added possibility to supply samples names as parameters in the URL. This will override sample column names from the VCF file.

comment:5 by Nicklas Nordborg, 13 months ago

In 7478:

References #1549: Add support for viewing variant details from the WGS variant calling

Addeds support for multiple samples in the "All" tab.

comment:6 by Nicklas Nordborg, 13 months ago

In 7479:

References #1549: Add support for viewing variant details from the WGS variant calling

Export "Description" from the meta-headers in the VCF file. The description is used as a hover text to display some information about each data field from the VCF.

comment:7 by Nicklas Nordborg, 12 months ago

Resolution: → fixed
Status: new → closed

comment:8 by Nicklas Nordborg, 12 months ago

In 7521:

References #1549: Add support for viewing variant details from the WGS variant calling

Displaying the ANN annotations as a separate table instead of a long string.

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