populationgenomics / automated-interpretation-pipeline

Rare Disease variant prioritisation MVP

MIT License

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Allow for interchromosomal split variants #367

Closed MattWellie closed 1 month ago

MattWellie commented 1 month ago

Fixes

366

Proposed Changes

Inter-chromosomal variants don't have a length. Instead, we set the 'SVLEN' to be 'chrX:12345' (the other side of the breakpoint)

Checklist

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

MattWellie commented 1 month ago

So will this make genie breakpoints in scope?

Yup! So long as the breakpoint causes an LoF annotation we're already picking them up... Unless this also fails in some new weird way