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I'm working on cancer samples run on illumina cytoSNP 850K array ( probes designed on GRCh38). I am trying to use PennCNV to detect the copy number variation from the data. Which hmm file would be app…
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When using same_type=1 all "INV" records (and other SO types) are skipped on the following line:
```
next if $olap_sv->class_SO_term() ne $svf->class_SO_term() && $self->{same_type} ==1;
…
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Dear dev community,
Would you consider building a container for [PennCNV tool](http://penncnv.openbioinformatics.org/en/latest/)?
Briefly, it is a free software tool for Copy Number Variation (CNV…
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Dear developer,
Thank you for your kind words and appreciation for this powerful tool. As an infercnv beginner, I have several doubts and areas where I lack understanding. I would like to seek your…
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### Is your feature related to a problem?
The ability to identify copy number variants from matched tumour and normal (_i.e._ non-tumour) samples having undergone whole genome sequencing with ONT seq…
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Related to: Provide an indication that staff are viewing a fully restricted item https://github.com/wellcomecollection/wellcomecollection.org/issues/11257
## Current solution
 for estimating repeat sizes
- [ ] [QDNAseq](https://github.com/ccagc/QDNAseq) CN…
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**What is this request referring to?**
Result of genomic copy number assessment of a genomic element or region
**What is the name you would like SO to give the term?**
`copy number assessment` an…
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Before GDC made the recent changes, I was able to get GISTIC scores with values such as -1, 0 and +1 using `Gene Level Copy Number Scores`. Now with the ASCAT copy number values, I am not sure how to …