{"architecture":{"family":"CNN over read-pileup images","input":"BAM/CRAM + reference","output":"VCF/gVCF"},"article":null,"cancer_slugs":["pan-cancer"],"category":"genomics","confidence":"high","datasets":[{"name":"Genome in a Bottle (GIAB)","note":"","role":"benchmark","slug":"giab-genome-in-a-bottle"}],"developer":"Google","evaluation":[{"benchmark":"PrecisionFDA Truth Challenge (2016)","external":true,"metric":"SNP/indel F1","source":"https://www.nature.com/articles/nbt.4235","value":"highest SNP accuracy award"}],"hf":null,"kind":"tool","license":"BSD-3-Clause","limitations":"- Germline-first; somatic calling needs DeepSomatic or a dedicated caller.\n- Model type must match the sequencing technology.","links":{"demo":null,"docs":null,"doi":"10.1038/nbt.4235","github":"https://github.com/google/deepvariant","huggingface":null,"paper":"https://www.nature.com/articles/nbt.4235","pmid":null},"modalities":["genomics"],"name":"DeepVariant","notable_uses":"","openness":"open-weights","regulatory":{"intended_use_en":"Research pipelines; clinical labs validate it inside their own accredited workflows.","intended_use_pl":"Potoki badawcze; laboratoria kliniczne waliduj\u0105 go we w\u0142asnych akredytowanych procesach.","source_url":"https://github.com/google/deepvariant","status":"research-only"},"regulatory_status":"research-only","release_date":"2017-12-04","run_snippet":"docker run -v $PWD:/data google/deepvariant:latest /opt/deepvariant/bin/run_deepvariant \\\n  --model_type=WGS --ref=/data/ref.fa --reads=/data/sample.bam \\\n  --output_vcf=/data/sample.vcf.gz --num_shards=8","settings":["diagnosis","basic-research"],"slug":"deepvariant","sources":[{"label":"Poplin R et al. A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol 2018","url":"https://www.nature.com/articles/nbt.4235"},{"label":"GitHub \u2014 google/deepvariant","url":"https://github.com/google/deepvariant"}],"summary":"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\u2013normal somatic variants.","tasks":["variant-effect","classification"],"training":{"summary_en":"Genome in a Bottle truth sets (NA12878 and others) across Illumina, PacBio and ONT sequencing.","summary_pl":"Zbiory referencyjne Genome in a Bottle (NA12878 i inne) dla sekwencjonowania Illumina, PacBio i ONT."},"updated_at":"2026-09-05T22:26:01.073559","url":"/ai-oncology/models/deepvariant","usage":{"library":"Docker image google/deepvariant","snippet":"docker run -v $PWD:/data google/deepvariant:latest /opt/deepvariant/bin/run_deepvariant \\\n  --model_type=WGS --ref=/data/ref.fa --reads=/data/sample.bam \\\n  --output_vcf=/data/sample.vcf.gz --num_shards=8"},"verified_at":"2026-09-05T22:26:01.073225","verified_by":"editorial","version":null,"what_it_does":""}