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### Need
MSI analysis was requested to be included to the workflow in https://github.com/Clinical-Genomics/BALSAMIC/issues/972
### Suggested approach
Add [MSIsensor-pro](https://github.com/x…
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### Need
The number of SVs uploaded to Scout for WGS cases in balsamic is much higher than is common, and could really benefit from being reduced. As an example here are the some values from the mo…
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### Description
It has been mentioned previously that our current methods for detecting CNVs are not working very well for low tumor purity samples: https://github.com/Clinical-Genomics/project…
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### Description of the bug
Samplesheets with more normal-samples per patient pass nf-validation, but they (probably) shouldn't.
https://nfcore.slack.com/archives/CGFUX04HZ/p1698056996871649?thread…
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As an example, (I hope that this Scout-link will persist): https://scout-stage.scilifelab.se/cust087/F0049453/sv/variants/8e2113f40646b16473f9a12af4e57e0b
This is one of the variants that we're loo…
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Good day,
I would like to know whether I can use your tool to check coverage in 10x genomics data. My aim is to check the coverage in some specific chromosomes per cluster. I have tumor samples and…
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### Need
As a clinician I want to be able to detect all true somatic variants, but currently in WGS-tumor-only cases we are filtering out all somatic variants with a VAF of 1 with a bcftools filter…
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Hi! Congrats for the study! Very nice!
I am integrating more data into your TICA atlas and I am following the approach you use here: https://github.com/Single-Cell-Genomics-Group-CNAG-CRG/Tumor-Imm…
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Hi,
I did not find the answer to this question. And I am not sure if this is something reasonable to do.
Can I use single cell data generated by SmartSeq as a normal reference to infer CNVs on 10x g…