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populationgenomics / production-pipelines

Genomics workflows for CPG using Hail Batch
MIT License
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gCNV JointSegmentation Issues #740

Closed MattWellie closed 1 month ago

MattWellie commented 4 months ago

https://batch.hail.populationgenomics.org.au/batches/445596

dodgy ploidy on chrY & X...

MattWellie commented 4 months ago

Cross-posted as https://github.com/broadinstitute/gatk/issues/8834

This looks to be a known issue, previously posted: https://github.com/broadinstitute/gatk/issues/8164

We were informed that this was fixed in 4.3.0.0. Narrator: it wasn't

I've re-run using 4.5.0.0 and it remains broken.