I assume this has never been tested.

[drtconway]

No description provided.

[illusional]

Thanks for the PR @drtconway.

In an earlier version it was flipped, and looks like two errors cancelled each other out during testing, when I corrected it 42caaa9 it looks like I've flipped it back to incorrect.

For transparency, we're currently upgrading both germline and somatic pipelines, with more QC and other tools to bring them more in-line with what is expected - and to use the latest Janis features.

We're also working on better release and testing processes to catch errors like these, because they're not acceptable.