BALSAMIC

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### Need Tumor purity is currently included in CNV report. There is a field in Scout for tumor purity, but the purity value is not added to the field. ###...

khurrammaqbool

[User Story] Improve CNV calling for target workflow

5

### Need As a clinical geneticist, I need an improved CNV workflow for targeted panel sequencing (UMI & non-UMI), in particular for cfDNA samples, to accurately detect genetic variations. ###...

ivadym

### Need We decided not to included FFPE samples to the current loqusDB databases and create new database using loqusDB instead. ### Suggested approach Create new set of database using...

khurrammaqbool

feat: add msi tn to storage

2

## Description Add MSI tumor-normal analysis output to the housekeeper storage. [PR description] #### Added - MSI tumor normal output to housekeeper storage. ## Documentation - [x] N/A - [...

khurrammaqbool

feat: merge vardict and tnscope

3

## Description This PR is a branch of: cnvkit_to_gens: https://github.com/Clinical-Genomics/BALSAMIC/pull/1448 --> Which is a branch of: update_cnvkit_pons: https://github.com/Clinical-Genomics/BALSAMIC/pull/1465 --> Which is a branch of: deduplicate_with_umi https://github.com/Clinical-Genomics/BALSAMIC/pull/1358 Part of the development...

mathiasbio

### Need As a customer ordering UMI analysis in balsamic which by default does 3,1,1 filtering on UMI family size I would like to save money on my order by...

mathiasbio

feat: add artefact database argument

2

## Description Adds argument and filtering of SNVs using a VCF with frequencies exported from a loqusDB instance containing somatic SNV variants called on merged WGS normal samples. #### Added...

mathiasbio

### Need As a clinician I want as many true variant calls as possible while avoiding false positives. VarDict has proven to be unreliable in both performance (crashing due to...

mathiasbio

chore: add QC criteria for lymphoma_MRD

2

## Description New lymphoma_mrd panel has been added to production and it needs a QC threshold: https://github.com/Clinical-Genomics/BALSAMIC/issues/1478 #### Added - QC threshold for lymphoma_MRD panel ## Documentation - [x] N/A...

mathiasbio

### Task We have a new bait set that we would like to add a QC criteria for. The bait set is "Lymphoma MRD" and the criteria should be PCT_TARGET_BASES_1000X...

moahaegglund