BALSAMIC

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### Need As a developer, I want to migrate Balsamic to Snakemake 8 to stay up-to-date with the latest features in Snakemake, ensuring that my bioinformatics analyses take full advantage...

ivadym

[User Story] Move QC validation to CG

2

### Need As a Balsamic developer, I want to simplify the QC extraction and validation workflow, so that I can efficiently manage the increasing complexity of various workflow types, panels,...

ivadym

### Need As a Balsamic developer, I would like the process of handling reference files from the CLI to be more straightforward. This improvement will help me efficiently manage and...

ivadym

### Need As a Balsamic external developer I would like to be able to install Balsamic using poetry, so that I can effortlessly manage dependencies in isolated environments (i.e. [Bianca](https://www.uppmax.uu.se/resources/systems/the-bianca-cluster/))....

ivadym

### Need As a Balsamic developer, I want to have enhanced flexibility and granularity in specifying computational resources for my rules. Currently, thread counts serve as the primary method for...

ivadym

### Need As a developer I want to spend less time solving obscure issues with the tools we are using, VarDict has had a history with us failing in strange...

mathiasbio

[User Story] Reduce number of false positive SVs by constructing an artefact database

1

### Need The number of SVs uploaded to Scout for WGS cases in balsamic is much higher than is common, and could really benefit from being reduced. As an example...

mathiasbio

### Need As a hospital geneticist diagnosing patients from TGA data I want to be able to detect common CNVs on as small a scale as possible. Currently CNVs are...

mathiasbio

### Need As a geneticist I want to be able to understand the quality of the variant calls I am interpreting. Currently in the UMI workflow we are only keeping...

mathiasbio

### Description Balsamic has included support for the dog-reference genome canfam3 for a long time but I haven't seen any sample being run through this reference. The question is if...

mathiasbio