Hi everyone
I am seeing inconsistent behavior with DeepVariant.
• Works fine on GIAB data
• On some datasets, DeepVariant shards take extremely long (up to 24h) or appear to stall
• Running on GCP (Google Batch), with intervals (~20+ shards), using 16 CPUs
What’s odd: the actual variant calling step seems fast, but total runtime is very long → possibly infrastructure-related?
Has anyone experienced this or has tips to optimize DeepVariant performance in Sarek?
Thanks 🙏