Opened 4 years ago

Last modified 4 years ago

#1200 closed enhancement

Release exporter changes due to Variant calling pipeline — at Version 4

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: Reggie v4.26
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

When the Variant calling pipeline has been fully implemented (#1199), we also need to update the release exporter plug-in to export some of the data.

Most annotations from the VariantCall raw bioassay should be exported:

  • VariantsPassedFilter
  • All annotations that are included in the VCALL_Release category. This category should be created by the installation, but annotations should be added manually.
  • And also some common techincal annotations: Pipeline, DataFilesFolder, Software

We should also export annotations from the Alignment:

  • CallableBases
  • VariantsRaw

Files:

  • variants-filtered.vcf
  • variants-annotated.vcf.gz

Change History (4)

comment:1 by Nicklas Nordborg, 4 years ago

Description: modified (diff)
Milestone: Reggie v4.x → Reggie v4.26

comment:2 by Nicklas Nordborg, 4 years ago

In 5873:

References #1200: Release exporter changes due to Variant calling pipeline

Added VariantCallingWriter. It should export the specified annotations and files now.

comment:3 by Nicklas Nordborg, 4 years ago

In 5875:

References #1200: Release exporter changes due to Variant calling pipeline

Export AlignmentName as an annotation for all raw bioassays to make it easier to connect data that has a common alignment (for example, StringTie and VariantCall).

Updated README with information about the 'variantcall.lst' file.

comment:4 by Nicklas Nordborg, 4 years ago

Description: modified (diff)
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