Documentation
September 9, 2025 ยท View on GitHub
Quick start and Case studies
- DeepVariant quick start
- DeepVariant whole genome case study
- DeepVariant exome case study
- DeepVariant PacBio case study
- DeepVariant ONT R10.4 simplex case study
- DeepVariant hybrid (PacBio and Illumina) case study
- DeepVariant Complete Genomics T7 case study
- DeepVariant Complete Genomics G400 case study
- RNA-seq Case Study for Illumina RNA-seq.
- PacBio Iso-Seq/MAS-Seq Case Study.
- Runtime and accuracy metrics for all DeepVariant models
- Best practices for multi-sample variant calling
- Using graph genomes: VG Giraffe + DeepVariant case study
- Pangenome-aware DeepVariant WGS: Mapped with BWA, Mapped with VG
- Pangenome-aware DeepVariant WES: Mapped with BWA
- Roche SBX case study
Visualization and analysis
- show_examples: Saving human-readable images from DeepVariant examples
- VCF stats report
- Runtime by region for make_examples
Colab notebooks
- Colab example: visualizing pileup images/tensors
- Google Developer Codelab: Variant Calling on a Rice genome with DeepVariant
(Advanced) Training
- Advanced Case Study: Train a customized SNP and small indel variant caller for BGISEQ-500 data
- DeepVariant training data
More details
- DeepVariant usage guide
- Building and testing DeepVariant
- DeepVariant Genomic VCF (gVCF) support
- Getting Started with GCP (It is not required to run DeepVariant on GCP.)