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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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Add MSI score for tumor-normal cases #4690

Closed khurrammaqbool closed 5 days ago

khurrammaqbool commented 5 days ago

Scout had a field to show MSI score. BALSAMIC added MSIsensor-pro to compute the MSI score that can now be added to Scout. image

Describe the solution you'd like MSIsensor-pro is added for tumor-normal cases in BALSAMIC workflows, which generates a TXT file given below:

Total_Number_of_Sites   Number_of_Somatic_Sites %
938254  10390   1.11

Where the last column (%) is the MSI score, which can be parsed to be shown in Scout.

Describe alternatives you've considered A clear and concise description of any alternative solutions or features you've considered.

Additional context Add any other context or screenshots about the feature request here.

dnil commented 5 days ago

Hi, you can find instructions on how to load the MSI value here: https://clinical-genomics.github.io/scout/admin-guide/load-config/, I guess for Balsamic passed on via CG here: https://github.com/Clinical-Genomics/cg/blob/bbe5c6d396a7d8fcc88dd24b3c3dfc9547d4bf19/cg/models/scout/scout_load_config.py#L70. Unless you want to parse other values from that file I don’t see a good reason to change the number on the sample level for a file name on the same and add a parser? Closing this for now, but don’t be afraid to argue it and reopen if I missed something! Cheers!