Raredisease add GC and AT dropout quality check #3838
Conversation
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| @staticmethod | ||
| def set_dropout_cutoff_by_analysis_type(sample: Sample, metric_conditions: dict) -> None: | ||
| if ( | ||
| sample.application_version.application.analysis_type | ||
| == SeqLibraryPrepCategory.WHOLE_GENOME_SEQUENCING | ||
| ): | ||
| metric_conditions["AT_DROPOUT"]["threshold"] = 5 | ||
| metric_conditions["GC_DROPOUT"]["threshold"] = 5 |
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This logic sets the treshhold for the AT and GC dropout to 5 in case of WGS. I think it would be better to pre-define a full set of Rare-disease WGS metrics and fetch the whole set of metrics when required.
I fear this logic here will be lost (especially if undocumented) later on. Whereas having two sets of QC threshold collections would be clearer. Plus, in case we would require other metrics with different tresholds we can modify the collection, rather than writing more functions with if statements.
My suggestion:
- Create RAREDISEASE_WGS_METRICS_CONDITIONS
- Create a function to `fetch_raredisease_metrics_conditions(prep_category)
- Use the set of fetched metrics
Description
In raredisease we want to add a GC dropout and AT dropout QC check to make sure we do not deliver low quality data. Details on the issue: https://github.com/Clinical-Genomics/MTP-RAREDISEASE/issues/25
Requested cutoffs by production management:
WES: 10 for GC and AT dropout
WGS: 5 for GC and AT dropout
Suggested solution here is to set the cutoff at 10 for all sample types, and if the analysis type of a sample is WGS, it will set them to 5.
Added
Changed
Fixed
How to prepare for test
uspaxaHow to test
cg workflow raredisease metrics-deliver amusingmarmoset, it should complete successfully.Expected test outcome
Review
Thanks for filling in who performed the code review and the test!
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Implementation Plan