Display RNA alignment data in snv/indels variants view on existing case
See original GitHub issueBackground 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:
- Created 3 years ago
- Comments:7 (3 by maintainers)
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Any cram file with RNA data would do right or does it have to be matched to a DNA cram?
The specifics for the splice junctions track in igv.js: https://github.com/igvteam/igv.js/wiki/Splice-Junctions