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feat: add tga cnvkit to gens #1448
base: update_cnvkit_pons
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At the moment the pipeline is working for the TGA workflows but i haven't verified all workflows yet. So at the moment we could just view this review as a code-review. |
Codecov ReportAll modified and coverable lines are covered by tests ✅
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Quality Gate passedIssues Measures |
GENS has previously only been activated for WGS in Balsamic, however with the inclusion of this PR into production Clinical-Genomics/BALSAMIC#1448 CNV and BAF profiles from TGA samples can be uploaded as well. This feature is planned for release 16.0.0 of Balsamic (somewhere around **August maybe**) and requires a couple of small changes in CG. ### Added - gnomad-af argument to TGA samples ### Changed - gens upload no longer filters out TGA samples
Description
This PR adds post-processing steps to CNVkit results from TGA to facilitate upload to GENS, which has previously only been possible for WGS via post-processing of the GATK CollectReadCounts output.
As the gnomad vcf is required as well for the creation of the BAF visualisation track in GENS the config and the GENS rule assignment has been modified to make it possible to use of these rules and references in TGA as well.
And additional little script was added to massage the CNVkit file tumor.merged.cnr into a GENS accepted format with different resolutions.
This PR closes this issue:
#1385
Open question to discuss: purity adjusted log2 coverage values
I have in this GENS post-processing also decided to take as input the tumor-purity from PureCN to modify the log2 coverage values to make the fold-changes more visible in low-purity samples. I don't know if this is recommended, however CNVs in low purity samples would be quite difficult to observe without it.
This change requires further changes in CG
We need 2 changes as far as I can tell at the moment:
PR in CG: Clinical-Genomics/cg#3361
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