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### Operating System
Other Linux (please specify below)
### Other Linux
rocky linux 8.9
### Workflow Version
v2.0.0-g52e3698
### Workflow Execution
Command line (Cluster)
### Other workflow ex…
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Hi everyone,
I am analyzing my scRNA-seq data and I have 12 samples. I have run inferCNV on each one of my samples and have all the results.
Now I want to combine all the results and draw a heatma…
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despite #262
we are still seeing some false inversions in regions of CNV, e.g.:
https://legumeinfo.org/gcv2/gene;lis=phavu.Phvul.003G002400?algorithm=repeat&match=10&mismatch=-1&gap=-1&score=30&thr…
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Add 7316-1106 and 7316-3000 back to hope subcohort, except for proteomics. Use the attached file from Pei.
[master_11032023 (1).txt](https://github.com/user-attachments/files/15892642/master_11032023…
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Hi,
Thank you for this tool to summarize the copy number for multiple sample. It works great!
I got a question. In my CNV analysis for loss, we have only deletion or deep deletion, which is 1 or…
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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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Hi,
I've encountered a sample where the CNV prediction throws an error. All other samples were processed fine. I couldn't find any (obvious) problems within the counts or the VCF file. The R-output i…
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When trying to call functions like `ag3.gene_cnv('AGAP001356')`, if there are any releases where CNV data is not yet available, this will generate a cryptic error message:
```
FileNotFoundError: '…
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Dear @tobiasrausch,
Hi. I'm Oh.
I executed the delly for Germline CNV calling.
I want to ask about the genotype of my called CNVs (c1.cnv.bcf), or merge the calls (merged.bcf).
```
re…
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Hello!
I'm attempting to run the tool with a matched tumor-normal sample but the _CNVs file that produces is lacking the end coordinate and the somatic/germline classification.
This is the confi…