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New RNA reports in Scout

See original GitHub issue

RNA data already supported by Scout:

  • A pdf report produced by Arriba, loaded at the case level, with the key gene_fusion_report (or gene_fusion_report_research if it’s based on research data) Suggested name: arriba_report
  • splice_junctions_bed and rna_coverage_bigwig -> igv tracks saved at the case.individual level

New reports and data to be included:

  • Another fusion report file in HTML format produced by FusionReport (this is the fusion summary that collects metrics from different methods: arriba, pizzly, starfusion, fusioncatcher, squid). This should be the primary summary report. Suggested name: fusion_report.
  • Another fusion report HTML file produced by FusionInspector (this provides a detailed visualization of all fusions found). Suggested name: fusion_inspector.
  • RNA multiqc file, also HTML file, work in progress, see #3650
  • .tsv file from Fusion Inspector -> convert into variants-like data and load as if they were scout variants

Issue Analytics

  • State:open
  • Created 10 months ago
  • Comments:7 (2 by maintainers)

github_iconTop GitHub Comments

northwestwitchcommented, Nov 8, 2022

I’ve merged the PR to simplify loading of case reports in Scout. Now we can basically add items to this list and the reports should be loaded with the command scout load report <report-type>.

I’m not sure if these reports will be loaded when provided in the case config file when loading/updating a case…

fevaccommented, Nov 8, 2022

Good point. I like that.

Read more comments on GitHub >

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