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Hi
I was just wondering, can you use Canvas to detect copy number variants from any WGS data? The manual and publication talks almost explicitly about tumor and normal samples. Shouldn't e.g. Somat…
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Hi Dr. Wang,
I noticed in the help message of the 'detect_cnv.pl', training optimized .hmm model parameters is not recommended. But I guess it would be better to train the model when the data is fr…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/zhouzilu/iCNV
Confirm the following by editing ea…
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@LeeTL1220 commented on [Mon May 23 2016](https://github.com/broadinstitute/gatk-protected/issues/524)
- [ ] File issues for evaluations (and make sure each evaluation is described, including ground …
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Hi There,
I was following PennCNV affy tutorial, after "Step 2: Split the signal file into individual files for CNV calling by PennCNV", I did "wc -l file.split1" to check the number of lines and fo…
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Hi Paul,
I launched a bunch of jobs to "short" and noticed that sometimes they instead launched to juplow. I just wanted to make you aware of this, I think they are running fine, but they are not n…
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Hi,
I am trying to use the Canvas tool for WGS CNV detection.
Instructions says we can download the hg19 reference fasta (and I hope xml file) using the https://illumina.box.com/CanvasPublic link,…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/bioinf-jku/panelcn.mops
Confirm the following by …
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In preparation to supporting R 3.4, we are migrating any non-bio-related packages over to the conda-forge channel. This issue aims to organize and track the progress.
Below are the results of:
`…
daler updated
7 years ago
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#109 highlighted some issues: namely, which tools to support tumor/paired calls.
There is a comprehensive list on BioStars (http://www.biostars.org/p/19104/), so the plan would be to evaluate which o…