BALSAMIC

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## Need There are certain aberrations whose detection is important for diagnosis: - Include VAF or supporting reads for SVs (in the context of KMT2A duplication): https://github.com/Clinical-Genomics/BALSAMIC/issues/1073 - Detection of...

fevac

**Describe the bug** During job submission to Slurm, a silent `KeyError` disrupts the process, causing incomplete job submissions. As a consequence, the automation for storing cases in CG fails. This...

ivadym

### Need Information extracted from [915829](https://clinical-scilifelab.supportsystem.com/scp/tickets.php?id=63646) Emma Tham requested to see the quality metrics of the UMI workflow after the UMI collapse. Since we are still running the other balsamic...

karlnyr

Include the analysis of signatures and MSI

5

Hi I wonder if it is possible to include in balsamic pipeline the analysis of signatures and MSI This is important for some pediatric cases thanks teresita

terestahl

Ideogram vizualisation in Scout from balsamic data (Myeloid panel)

9

Hi, this is a feature request for the scout visualisation of genetic data from BALSAMIC (Myeloid panel). I just saw a new scout feature for MIP data that allows to...

genecracker

Sorry if this is a duplicate; since we couldn't find the issue this morning, I'm adding it here! **Describe the bug** GenMod family/case id is missing from rank score in...

dnil

create artificial truth-set for validation and variant-calling optimisation

2

**Is your feature request related to a problem? Please describe.** At the moment there are many validation-samples used in verifying the quality of the new releases of balsamic, however the...

mathiasbio

## Need Background, this issue was made to remove triallelic sites as a filter: https://github.com/Clinical-Genomics/BALSAMIC/issues/986 This PR was made to implement this: https://github.com/Clinical-Genomics/BALSAMIC/pull/1089 The solution was to change: `bcftools view...

mathiasbio

## Need In order to make multiqc pick up the Sentieon Dedup metrics file containing the PERCENT_DUPLICATES I had to trick it that it was a report from picard markduplicates...

mathiasbio

## Need There been some updated example pipelines on the Sentieon github since we last updated Sentieon, for example here: - https://github.com/Sentieon/sentieon-scripts/blob/master/example_pipelines/somatic/TNscope/default.sh - https://github.com/Sentieon/sentieon-scripts/blob/master/tnscope_filter/tnscope_filter.py Which we could draw inspiration from...

mathiasbio