populationgenomics / automated-interpretation-pipeline

Rare Disease variant prioritisation MVP

MIT License

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GATK-SV Category #338

Closed MattWellie closed 6 months ago

MattWellie commented 6 months ago

Fixes

AIP doesn't yet support SV variants

Proposed Changes

Introduces optional additional processing of an annotated GATK-SV MT
Introduces a new category SV1 (LOF in green gene)
Variant labelling and MOI testing process treats small variants and SVs as equivalent
SVs are treated differently in HTML presentation (links, annotations, TX consequences)

Not Yet Incorporated

complex GT testing (i.e. if a small variant and a deletion are overlapping, treat Hom calls as Het)
various GT test cases around overlapping/compound het variants

Checklist

[x] Related Issue created
[ ] Tests covering new change
[x] Linting checks pass