BALSAMIC

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**Description** It was pointed out in that the current etiquette makes the rule names long. It will be nice to make it more comprehensive, meaningful and shorter by making it...

khurrammaqbool

Fix detect optical duplicates in TGA workflow

2

## Need Related to this issue: https://github.com/Clinical-Genomics/BALSAMIC/issues/1282 Optical duplicates have not been detected and traced in the TGA workflow due to the presence of UMI tags in the read header...

mathiasbio

Upload soft-filtered variants to Scout?

3

**Is your feature request related to a problem? Please describe.** In a validation of the GMS Lymphoid panel there's been a few variants in the reference samples that were filtered...

mathiasbio

[User Story] Record optical duplicates in QC report

8

## Need As the lab head of unit I want to be able to trend the optical duplicates in samples processed by BALSAMIC so that we can see if the...

pbiology

### Need As a Balsamic developer, I want to improve the codebase by refactoring existing code to enhance maintainability, readability, and performance, ensuring the long-term sustainability of the pipeline. ###...

ivadym

### Need As a geneticist doing variant interpretion I want to be able to easily and accurately evaluate the effect of the mutation on the gene. With the new update...

mathiasbio

[Assessment] Does using call-regions option Manta allow for variants with only 1 BND in target-bed?

2

### Description Manta has an option to use `--call-regions` argument and supply a bedfile to restrict the calling of variants to within this region. This sounds good for our TGA...

mathiasbio

### Need As a bioinformatician I want sex-specific panel of normals to improve accuracy of CNV calls, be able to capture genomic sex differences and to comply with bioinformatic best-practices...

fevac

[Assessment] Include columns for SNVs showing LoH / CNV in new TGA CNV PDF

1

### 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,...

mathiasbio

### Need As a developer, I want to simplify the process of installing Balsamic on Hasta by providing a script that automates this step. This will save time and ensure...

ivadym