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Hi, I am trying to run spectre for CNV analysis for my targeted cancer data. I am getting the following error.
My command line:
spectre CNVCaller \
--coverage s101.regions.bed.gz \
--sample-i…
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inferCNV uses a [hidden markov model](https://github.com/broadinstitute/inferCNV/wiki/inferCNV-HMM-based-CNV-Prediction-Methods) to turn the smoothed gene expression into genomic regions that are subj…
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Hello,
I have been using Numbat for quite sometime now, and it has worked great. Recently we switched to the 5' 10X protocol. Numbat fails to correctly identify the CNVs, and in all samples i keep …
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Looking good!
You can add an example PNG into the Readme like so
![example cnv plot](https://github.com/Adoni5/cnv_from_bam/blob/10a2b00a8832b46cacbff0e2f775a4f440844da0/example_cnv.png?raw=true…
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#### What data file(s) does this issue pertain to?
`cnv-controlfreec-tumor-only.tsv.gz`
#### What release are you using?
v13-v15
#### Put your question or report your issue here.
The st…
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### Description
Clinicians need to be able to detect LoH and CNV in TGA cases. Currently a CNV report is produced which contains diagrams and tables for CNVs and LoH, CNVs are also in the SV VCF file…
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![image](https://github.com/malariagen/malariagen-data-python/assets/34922269/10ae5217-3cbf-4979-8134-c61c11ca33cd)
There are no CNV calls for this sample set so it fails. Earlier versions of the d…
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I've attempted to install cnv_facets package using:
```
conda create -n facets
conda activate facets
conda install -c bioconda -c conda-forge cnv_facets
```
It's taking forever to install and …
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Hello,
I found that some CNV calls involving two genes had different result between full vs split mode. Full mode returned NaN, while one of the split call predicted frameshift correctly. Is this be…
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Hello!
For a few of my samples I keep getting this error message without it reporting any data:
NOTICE: All program notification/warning messages that appear in STDERR will be also written to log…