BALSAMIC

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feat: replace vardict with tnscope

1

## Description This PR is a branch of: deduplicate_with_umi (https://github.com/Clinical-Genomics/BALSAMIC/pull/1358) Which is a branch of: Update sentieon: (https://github.com/Clinical-Genomics/BALSAMIC/tree/update_sentieon) This PR replaces VarDict with TNscope and cleans up the snakemake rules...

mathiasbio

feat: use UMIs in TGA workflow

1

## Description This is an alternative solution to the one implemented here: https://github.com/Clinical-Genomics/BALSAMIC/pull/1358 And it aims to introduce the same feature but with different approaches. The previous approach tried to...

mathiasbio

[User Story] Deduplication with consensus collapse

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### Need As a clinician I want to be able to detect variants to a low allele frequency, as cheaply as possible, and with as few false positives as possible....

mathiasbio

feat: deduplicate with UMIs

3

### This PR: **Blocked by:** - Update Sentieon: https://github.com/Clinical-Genomics/BALSAMIC/issues/1384 This update requires updating Sentieon as the current version in production: `sentieon-genomics-202010.02` Does not contain the consensus option for LocusCollector which...

mathiasbio

chore: Update development versions & GitHub Actions

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## Description As we need to bump black version due to security issues: https://github.com/Clinical-Genomics/BALSAMIC/pull/1420, I've also took the opportunity to update the dev requirements and update GitHub Action versions ####...

ivadym

feat: update sentieon to version 202308.02

2

## Description This PR does not aim to include many updates in terms of analysis, but mainly serve to verify the continued integrity and performance of the workflows after updating...

mathiasbio

[User Story] Create TNscope PON

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### Need As a geneticst, despite not having a matching normal sample for germline filtering, I want to be sure that all somatic variants I am interpreting are true somatic...

mathiasbio

[User Story] Update Sentieon

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### Need As a hospital geneticist I want: - As many true variants as possible with as few false positive variants - As fast as possible - And as cheaply...

mathiasbio

feat: Remove GATK3

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## Description Remove GATK3 from the workflow [PR description] #### Removed - GATK3 from the workflow and from the container - ## Documentation - [x] N/A - [ ] Updated...

khurrammaqbool

[User Story] Quick adjustments of QC thresholds

2

### Need As a production bioinformatician I want to avoid handling failing samples as much as possible, and quite frequently samples fail QC-metrics that are then set to PASS regardless....

mathiasbio