Change Vapor bed preprocessing errors to warnings

broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing

BSD 3-Clause "New" or "Revised" License

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Change Vapor bed preprocessing errors to warnings #622

Closed mwalker174 closed 6 months ago

mwalker174 commented 7 months ago

These errors are being triggered on allosome contigs, i.e. chrY in female samples. We can leave them in as warnings but they aren't strictly necessary.

Tested with a docker rebuild on a few samples that then completed successfully.