BALSAMIC

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### Description In conjunction with developing a PR for changing filters and settings for variants called with Manta, I reached out to one of our customers to ask if they...

mathiasbio

add soft normal-filtered VCF

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## Description [PR description] #### Added - [Description] #### Changed - [Description] #### Fixed - [Description] #### Removed - [Description] ## Documentation - [ ] N/A - [ ] Updated...

mathiasbio

[Assessment] CNV calling in low purity samples

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### Description It has been mentioned previously that our current methods for detecting CNVs are not working very well for low tumor purity samples: https://github.com/Clinical-Genomics/project-planning/issues/447 This needs to be assessed...

mathiasbio

### Description The intermediate multiqc files store sample specific information using keys that are not always solely the sample id. For example the file: `multiqc_picard_wgsmetrics.json` contains a key field named:...

ChrOertlin

### Need As a developer I want to generate all BALSAMIC panel of normals using the [nf-core createpanelrefs pipeline](https://nf-co.re/createpanelrefs/dev) so I don't have to maintain PON generation workflows in BALSAMIC...

pbiology

Tumor mutation burden

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## Need ### TMB calculation today in BALSAMIC The current definition is based on: 1. TMB was defined as the number of somatic, coding, base substitution, and indel mutations per...

pbiology

**BALSAMIC version** 10.0.2 **Current affected rule if snakemake workflow related** vcf2cytosure generation for wgs singleton (and perhaps a couple of others?) use single caller SV VCFs for aberration generation, even...

dnil

## Need Some variants/genes should be filtered out ## Suggested approach *A few sentences about the intended solution* ## Considered alternatives *Were there alternative approaches which have been rejected?* ##...

pbiology

## Need *In a short and concise manner, describe the need the feature satisfies* ## Suggested approach *A few sentences about the intended solution* ## Considered alternatives *Were there alternative...

pbiology

[User Story] Fix recurrent problems with BALSAMIC containers

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### Need As a BALSAMIC developer, I want the recurrent container issues and failures to be resolved so that I can experience improved efficiency and reliability in testing and deploying....

ivadym