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Display RNA alignment data in snv/indels variants view on existing case

See original GitHub issue

Background When analysing an individual it is common to start with a DNA analysis. However, often a causative variant is not found and the same individual also are subjected to a RNA analysis.

Challenge Currently, there is no way to combine the output from the standard DNA analysis with the alignment output from a RNA analysis in Scout. It would be great to be able to update the DNA snv/indel view with alignment information for the RNA analysis in the form of a Sashimi plot: https://software.broadinstitute.org/software/igv/Sashimi. So when clicking the IGV (RNA) button you can go directly to a Sashimi plot of the gene(s) in question to look at the splice junctions across the samples in the case.

Suggested solution

  • Add the option in scout update case to also be able to upload a link pointing to an alignment file (BAM|CRAM + index) from a secondary analysis to an already existing case.
  • Also support this from the scout load config
  • Add button for RNA Sashimi plots in IGV on the snv/indel variants view

Issue Analytics

  • State:closed
  • Created 3 years ago
  • Comments:7 (3 by maintainers)

github_iconTop GitHub Comments

1reaction
jemtencommented, Feb 15, 2021

Any cram file with RNA data would do right or does it have to be matched to a DNA cram?

1reaction
northwestwitchcommented, Feb 9, 2021

The specifics for the splice junctions track in igv.js: https://github.com/igvteam/igv.js/wiki/Splice-Junctions

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