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Hi, thank you for this amazing package!
I have tried running STInferCNV with random_trees but it is taking way too long even with CPUs = 30 in my University's cluster. Is there another way to reduc…
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### Description of feature
Generate tumour-only mode for variant calling. This should only affect to the `variant_calling` module of the pipeline, once we obtain the VCFs the rest of modules should b…
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This command returns a clear BCL6::MYC event:
```
sv_data
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I am calling CNVs in tumour ONT long-reads and want to try using spectre
I assume it is preferred to input SNPs from a matched tumour sample rather than germline SNPs? Or would germline SNPs be mor…
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Hi,
I have tried "runPipeline --datahub breast-tumour-segmentation --file my_slide.svs". But none results are saved. Could you please provide a full command or python codes to segment a testing WSI…
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Helllo,
I'm facing this error with new version 2.1.0?, I'm analysing tumour WGS, job failed after 9hrs running with 48 cores. It would be great any help on this!! Many thanks for your support & dev…
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Hello,
When I run the given examples, I get a difference between tumour location specified and tumour location simulated. Could this offset be due to imaging domain having pixels outside the scope …
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Hello!
We are working on a longitudinal study of tumour samples (we have samples at different time points for each donor) and we want to analyze their clonal evolution.
We have read in your paper …
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Questions to be added:
- [x] ~Which tumour sample has more mutations?~
- [ ] Which of the following mutations is a driver in the tumour from patient A?
- [ ] Which tumour sample has more drivers?
- […
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Hi, is it possible that the snakemake implementation supports single "tumour-only" samples? It looks as though it doesn't, or at least this usage is not described. I am making a snakemake workflow em…