Opened 11 months ago

Closed 6 months ago

#1200 closed enhancement (fixed)

Release exporter changes due to Variant calling pipeline

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 (6)

comment:1 Changed 6 months ago by Nicklas Nordborg

Description: modified (diff)
Milestone: Reggie v4.xReggie v4.26

comment:2 Changed 6 months ago by Nicklas Nordborg

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 Changed 6 months ago by Nicklas Nordborg

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 Changed 6 months ago by Nicklas Nordborg

Description: modified (diff)

comment:5 Changed 6 months ago by Nicklas Nordborg

In 5880:

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

Added a category VCALL_Release for annotation types that should be exported together with VariantCall raw bioassays. Annotation types need to be added to this category manually. This means that none of the MutationSignatureNN or GENE_Variants are exported automatically.

comment:6 Changed 6 months ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed
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