Opened 6 months ago

Closed 4 months ago

#1543 closed task (fixed)

Release exporter changes due to WGS data

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.51
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

We should include some WGS data in the next release. The starting point is existing BloodDNA (normal) and DNA (tumor) items that are already included in the release.

From the DNA items we go down to Library items. Extra aliquots inbetween are skipped.

From Library we skip the MergedSequences and go directly to AlignedSequences.

Then, we can add both CopyNumber items and VariantCall items as child items to the AlignedSequences items.

Relevant annotations should be included in the release. From library:

  • Pipeline
  • ExternalOperator

From alignments:

  • Pipeline
  • DataFilesFolder
  • ALIGNED_BASES
  • ALIGNED_PAIRS
  • FRACTION_DUPLICATION
  • FRACTION_OPTICAL_DUPLICATION
  • FragmentSizeAvg
  • FragmentSizeStdev
  • MEAN_COVERAGE
  • SD_COVERAGE
  • PF_BASES
  • PF_Q30_BASES
  • QC_GenoTypeHET_PCT
  • AlignmentSoftware
  • READS (from the parent MergedSequences)

Files that should be included from alignments items:

  • alignment.bam
  • alignment.bai

From ASCAT items:

  • Pipeline
  • DataFilesFolder
  • ImbalanceTest
  • Penalty
  • PsiManual
  • RhoManual
  • TauManual
  • Ploidy
  • Purity
  • NormalContamination
  • GoodnessOfFit
  • GI_Score
  • LOH_fraction
  • NonAberrant

Files from ASCAT items:

  • ASCATprofile.png
  • ASPCF.png
  • germline.png
  • normal_baf.txt
  • normal_logr.txt
  • rawprofile.png
  • segments.txt
  • segments_raw.txt
  • stats.txt
  • sunrise.png
  • tumor.png
  • tumor_baf.txt
  • tumor_logr.txt

From VariantCall items:

  • Pipeline
  • DataFilesFolder
  • CallableBases
  • PanelOfNormals
  • VariantsRaw
  • VariantsPassedFilter
  • Variants_FDR_Est
  • Variants_Sensitivity_Est
  • Variants_FP_Est
  • Variants_FN_Est
  • VariantsFilterThreshold
  • F_SCORE_BETA

Files from VariantCall items:

  • variants-somatic.vcf.gz
  • variants-somatic.vcf.gz.tbi
  • filtering-stats.txt
  • segments.table
  • SBS_96.txt
  • SBS_96.pdf

Change History (19)

comment:1 by Nicklas Nordborg, 6 months ago

In 7454:

References #1543: Release exporter changes due to WGS data

Added Library items from the WGS pipelines to the release exporter.

comment:2 by Nicklas Nordborg, 6 months ago

In 7455:

References #1543: Release exporter changes due to WGS data

Added Aligned items from the WGS pipelines to the release exporter, but only a limited number of annotations so far.

Files are currently written to the same same sync scripts as the other files, but this need to be split since the WGS data is on a different server.

comment:3 by Nicklas Nordborg, 6 months ago

In 7456:

References #1543: Release exporter changes due to WGS data

The export now create two versions of each script. It is also possible to have different locations for script and data, but it is not yet implemented in the plug-in.

comment:4 by Nicklas Nordborg, 6 months ago

In 7457:

References #1543: Release exporter changes due to WGS data

Added a new FileServer item for DNA WGS release data.

comment:5 by Nicklas Nordborg, 6 months ago

In 7458:

References #1543: Release exporter changes due to WGS data

Added more annotations to the WGS alignment export.

comment:6 by Nicklas Nordborg, 6 months ago

Description: modified (diff)

comment:7 by Nicklas Nordborg, 6 months ago

In 7459:

References #1543: Release exporter changes due to WGS data

Added CopyNumber (ASCAT) items to the export. Annotations, files and connections to parent items are not yet included.

comment:8 by Nicklas Nordborg, 6 months ago

In 7460:

References #1543: Release exporter changes due to WGS data

Added more annotations and files to CopyNumber items.

comment:9 by Nicklas Nordborg, 6 months ago

Description: modified (diff)

comment:10 by Nicklas Nordborg, 6 months ago

In 7461:

References #1543: Release exporter changes due to WGS data

Added parent items for CopyNumber items. Note that there are two parents (one tumor and one normal alignment). This is currently not supported by the importer on the Relax side so we need changes there as well.

comment:11 by Nicklas Nordborg, 6 months ago

In 7467:

References #1543: Release exporter changes due to WGS data

File server information is exported for files.

comment:12 by Nicklas Nordborg, 6 months ago

In 7468:

References #1543: Release exporter changes due to WGS data

Added WGS variant call items to the export. Still missing a link back to the normal alignment.

comment:13 by Nicklas Nordborg, 6 months ago

Description: modified (diff)

comment:14 by Nicklas Nordborg, 6 months ago

In 7469:

References #1543: Release exporter changes due to WGS data

Include a link to the normal alignment when exporting WGS variant call.

comment:15 by Nicklas Nordborg, 5 months ago

Description: modified (diff)

comment:16 by Nicklas Nordborg, 5 months ago

In 7487:

References #1543: Release exporter changes due to WGS data

Include new annotations from the filter-stats.txt (see #1551) file in the release data.

comment:17 by Nicklas Nordborg, 5 months ago

In 7496:

References #1543 and #1554. Include the SBS counts and PDF plot in the release export.

comment:18 by Nicklas Nordborg, 5 months ago

Description: modified (diff)

comment:19 by Nicklas Nordborg, 4 months ago

Resolution: fixed
Status: newclosed
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