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I did
```r
library(TCGAbiolinks)
query_cnv In addition: Warning message:
> In rep(no, length.out = len) : 'x' is NULL so the result will be NULL
Debugging GDCprepare found out the error is com…
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I have adjusted the CNV using calculate-cnv, segment-cnv, and correct-cnv. After that, I was trying to see in the triangular plot of the cool file at the same region. Basically, it calculated chr5 at …
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Dear authors,
I successfully ran Numbat on multiple samples, however in some cases I would need to refine the tumor/normal definition (or eventually remove "noisy" CNV calls such as the BAMP). In th…
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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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Hi, I used Sequenza to obtain the cellularity of adjacent and tumor tissues, using normal BAM files from white blood cells. I have a question: why is the cellularity of adjacent tissues higher than th…
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Dear @readmanchiu,
The [Variant Call Format Specification v4.4. and v4.5](https://samtools.github.io/hts-specs/VCFv4.5.pdf) were released recently. One of the major changes is support for (short) t…
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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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This is more of a request, but I am trying to use the CNV track for visualizing genome-wide QTL.
The issue I'm having is that it accepts only one color instead of a vector of colors, so all radial …
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**Work on this ticket at the same time as #23382.**
There are 8 name request types for conversion (CNV):
1. BECR - Benefit Company → BC Limited
2. BECV - BC Limited → Benefit Company
3. CCV - BC Lim…
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Talked to Lucas and Kerryn about CNV classifications
They use [2020 ACMG CNV guidelines](https://pubmed.ncbi.nlm.nih.gov/31690835/)
Biggest questions are:
* Is gene LOF
* If CNV is not whole gene, t…