deepvariant

DeepVariant subworkflow

flowchart TD
  aBAM[/"HiFi aBAM"/] --> make_examples["DeepVariant make_examples"]
  make_examples --> gpu{"gpu?"}
  gpu -- yes --> call_variants_gpu["DeepVariant call_variants_gpu"]
  gpu -- no --> call_variants_cpu["DeepVariant call_variants_cpu"]
  call_variants_gpu --> postprocess_variants["DeepVariant postprocess_variants"]
  call_variants_cpu --> postprocess_variants
  postprocess_variants --> vcf[/"small variant VCF"/]
  postprocess_variants --> gvcf[/"small variant gVCF"/]

Loading

This subworkflow runs the three steps of DeepVariant individually in order to make best use of resources. If a GPU is available and gpu==true, the call_variants step will run on 1 GPU and 8 cpu threads, otherwise it will run on 64 CPU threads. The make_examples and postprocess_variants steps will always run on the CPU.