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## Description
TNscope VCF is missing GQ-values. Therefore, SNVs are not being uploaded to the `loqusdb-somatic` database.
It has been solved in Loqusdb side in https://github.com/Clinical-Geno…
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## Need
Customers have requested GENS to be implemented for Balsamic. GENS is a tool basically for viewing copy-number alterations and regions with LoH.
Originally developed in Lund, it has bee…
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Good day,
I am having an error when reaching step 17. I am using 10x genomics v3 data and use the raw count matrix as input. Below the code I used and the error:
Command:
```
infercnv_obj = i…
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## Need
Alt_allele_in_normal in TNscope seems way too strict in filtering out the presence of the tumor in the normal. Sometimes even a sequencing error of 1 base can be enough to set this filter. …
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## Need
Background to this feature can be found here: https://github.com/Clinical-Genomics/BALSAMIC/issues/1166
In short the need is to remove this filter `--exclude 'FORMAT/AF[0] > 1.0' --soft-…
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Cluster of RAB40B and XLOC_I2_008134 have the opposite phenotypes of a cluster of PIK3R3 and INSYN1 - googled most connections and got nothing so it may be novel.
Emailed Scott Soderling Duke Dec 1 h…
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## Describe the issue
I am trying to run the VEP tool in Nextflow as a docker image by specifying my own cache directory using the `--dir_cache` parameter. The directory exists outside. However, wh…
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**Background**:
- **cBioPortal:** cBioPortal is an open-source platform for cancer genomics data analysis and visualization. It provides a centralized resource for exploring and analyzing large-sc…
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## Need
`BALSAMIC ` adds `SOMATICSCORE` to the final SV `VCF` (*.clinical.filtered.pass.vcf.gz). This final `VCF` file is then uploaded to scout. `SCOMATICSCORE` is computed by manta for tumor-norma…
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### Description
After the changes to the core pipeline in V13.0.0 a substantial increase in Manta variants has been observed.
This can be read up on a bit more in the "Number of variants" sectio…