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In the paper it showed cnvnator in germline,but no in somatic, does this imply that canvas weaker in somatic than cnvnator, thanks, I just want to know the truth, both authors are definitely respectab…
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Greetings,
I have a paired somatic pipeline and two of the callers it uses are vardict and varscan2, which will output germline calls as well. I wanted to include them into my VLR candidates beca…
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Thanks a lot for updating such a powerful tool continously
in the cnvkit docs, it recommend theta2, and give the command. but in fact the theta2 has someproblems and the author does not recommend usi…
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Hi
I've noticed that the majority of my samples (WES, ~60-250x) are being predicted to have ploidy=2.00, purity=NA. I understand that this can happen when there's a lack of copy numbers but my sample…
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Hi,
I got geneLevel CN (copy number) by using cnvkit based on WES data (20 tumor samples unmatched normal). In result, I found a clear discrepancy between geneLevel CN from WES (cnvkit) and geneL…
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Hi Bcbio Team,
Do you know why the PURPLE does not recognize the -baf? I've checked bcbio PURPLE script [https://github.com/bcbio/bcbio-nextgen/blob/86edda9bedb3e90b814b0c54f3efb74fdf23aba8/bcbio/s…
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Hi everyone,
Can I use this workflow for tumor only variant calling to detect both Somatic and Germline variants? Or should I first run my data with Mutect in tumor only mode and then use varlocira…
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Long TODO lists don't get done.
We are trying to keep an issue open if a real effort is happening to resolve it.
The below priority list gives a sense of where bcbio is heading in the next two rele…
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Thank you for your tool. I have found Purple to give accurate results for most samples I have tested it on.
I have a sample that I am able to run Purple on successfully without using somatic SNVs, …
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# Balsamic Verification Report
## Release Information
- Version: `v14.0.1`
- Release Type: `Patch`
- Release Commit: b94831b
- Release Date: 2024-03-19
## Person(s) involved in the develo…