BALSAMIC

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### Description The current QC thresholds in BALSAMIC result in an increased and unnecessary burden on the production workflow which increases TAT and makes the work more tedious. We need...

mathiasbio

feat: change samtools stats to run per lane

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### This PR: This change may be requested in order to get alignments stats per lane, which could be more informative for the QC project Arnold/Maven. Added: for new features....

mathiasbio

Add resort bam

2

### This PR: (If this is a release PR, no need to add following. Leave this part empty) (Use the following lines to create a PR text body. Make sure...

mathiasbio

fix: TGA optical dup detection

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### This PR: Relevant feature issue: https://github.com/Clinical-Genomics/BALSAMIC/issues/1291 And associated QC metric issue: https://github.com/Clinical-Genomics/BALSAMIC/issues/1282 The aim of this PR is to fix the issue where optical duplicates are not detected in...

mathiasbio

### Need As a clinician I want high quality variant calls, and if the reads used for SV calling came from UMI collapsed reads some false positives may be removed....

mathiasbio

### Description I was curious about the extra environmental variables defined in the rule: `sentieon_bwa_umiextract` ``` export LD_PRELOAD={params.sentieon_install_dir}/lib/libjemalloc.so.1 export MALLOC_CONF=lg_dirty_mult:-1 ``` It seems that Sentieon recommends installing this library and...

mathiasbio

**Is your feature request related to a problem? Please describe.** In ticket: https://clinical-scilifelab.supportsystem.com/scp/tickets.php?id=61852 A customer mentioned that they had seen improved results over CNVkit with WisecondorX linked below: https://github.com/CenterForMedicalGeneticsGhent/WisecondorX Is...

mathiasbio

Look over UMI pipeline

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**Is your feature request related to a problem? Please describe.** **Initial ticket** False positive calls in UMI pipeline: https://clinical-scilifelab.supportsystem.com/scp/tickets.php?id=63493 **Background** Zahra has done extensive reporting on test-cases of reference-samples with...

mathiasbio

[User Story] Variants with VAF of 1 should not be automatically filtered out

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### Need As a clinician I want to be able to detect all true somatic variants, but currently in WGS-tumor-only cases we are filtering out all somatic variants with a...

mathiasbio

[User Story] Tools version tracking in delivery report

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### Need As a Balsamic user I want the delivery reports to clearly indicate the tools used during the analysis, so that I can have full transparency into the methodology...

pbiology