BALSAMIC
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Clinical-Genomics
Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
### Description A couple of WGS cases have now been unable to complete in the DNAscope gnomad rule which creates a BAF file to be used as input in GENS....
### Need As a clinical geneticist I would like to be able to identify Homologous Recombination Deficiency in our samples. "Homologous recombination deficiency (HRD) can arise from germline or somatic...
## Need SNV vcfs are annotated using the VEP plugin SpliceAI **Information:** https://github.com/Ensembl/VEP_plugins/blob/release/110/SpliceAI.pm https://pypi.org/project/spliceai/ ## Suggested approach Use the VEP module spliceAI with the final vcf files. Similar to how...
### Need As a geneticist I want to see true variants and not false positive calls. Currently we have databases for annotating variants that are commonly observed as somatic in...
### Need Structural variant filtering strategy was developed and discussed [here](https://docs.google.com/document/d/1D0fagdk6IKBOreiKpZAO5FBz00Qhk55gd1T17I6yrxs/edit). Some parts are implemented and the remaining parts required implementing a unified filtering method after addition of SV callers...
### Description During integration tests of balsamic 15.0.0: https://github.com/Clinical-Genomics/BALSAMIC/pull/1422 the test WGS T+N case did not finish running. One identified issue there was that GENS files are provided to hg38...
## Need To reduce the number of variants uploaded to scout, we should filter out the one that comes from local technical artefacts. ## Suggested approach Use LocusDB to remove...
## Need oncoBB annotation in BALSAMIC output. **Information:** https://www.oncokb.org/ ## Suggested approach *A few sentences about the intended solution* ## Considered alternatives *Were there alternative approaches which have been rejected?*...
### Need - As a user, I have noticed confusing parts in the documentation that need urgent improvements for a better experience. I suggest clarifications to enhance usability. - As...
### Need As a hospital administrator I want the pipeline to use GATK version 4 rather than 3 as the license for GATK 4 is free to use, but GATK...
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Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer