Cancer3.AI › AI in Oncology › AI Models › DeepVariant
Tool Open weights Research use only genomics

DeepVariant

Deep-learning variant caller that turns aligned sequencing reads into pileup images and classifies genotypes with a CNN; widely used for germline calling, with the companion DeepSomatic extending the approach to tumour–normal somatic variants.

GitHub Paper DOI { } JSON

At a glance

DeveloperGoogle
Released2017-12-04
LicenceBSD-3-Clause
AvailabilityOpen weights
KindTool
Regulatory statusResearch use only

What it does

Not yet documented on this card.

Tasks, data types and cancers

TaskVariant effectClassification
Data typeGenomics (DNA)
Clinical settingDiagnosisBasic research
CancerPan-cancer
InputBAM/CRAM + reference
OutputVCF/gVCF

Architecture

FamilyCNN over read-pileup images

Training data

Genome in a Bottle truth sets (NA12878 and others) across Illumina, PacBio and ONT sequencing.

Linked datasets

Evaluation

Benchmark / datasetMetricValueExternal validationSource
PrecisionFDA Truth Challenge (2016) SNP/indel F1 highest SNP accuracy award yes Source

How to run

docker run -v $PWD:/data google/deepvariant:latest /opt/deepvariant/bin/run_deepvariant \
  --model_type=WGS --ref=/data/ref.fa --reads=/data/sample.bam \
  --output_vcf=/data/sample.vcf.gz --num_shards=8
LibraryDocker image google/deepvariant

Regulatory status and intended use

Regulatory statusResearch use only
Intended useResearch pipelines; clinical labs validate it inside their own accredited workflows.

Source →

Regulatory status is quoted from the source linked above and can change. Research-use-only models must not be used for clinical decisions.

Limitations and bias

  • Germline-first; somatic calling needs DeepSomatic or a dedicated caller.
  • Model type must match the sequencing technology.

Sources

  1. Poplin R et al. A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol 2018
  2. GitHub — google/deepvariant

This page is educational — it is not medical advice and does not replace consultation with an oncologist. Diagnostic and treatment decisions are made solely by specialist physicians.