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broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing
BSD 3-Clause "New" or "Revised" License
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CPX_TYPE for CTX #664

Closed epiercehoffman closed 3 months ago

epiercehoffman commented 6 months ago

The CPX_TYPE for CTX records should be CTX_PP/QQ or CTX_PQ/QP. This is expected by downstream tools like ManualReview.wdl and SVAnnotate. In a recent callset, it was observed that the CPX_TYPE for CTX records was CTX. We need to investigate where this annotation is getting dropped.