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DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file.

DeepVariant supports germline variant-calling in diploid organisms.

Please also note:

DeepTrio

DeepTrio is a deep learning-based trio variant caller built on top of DeepVariant. DeepTrio extends DeepVariant's functionality, allowing it to utilize the power of neural networks to predict genomic variants in trios or duos. See this page for more details and instructions on how to run DeepTrio.

DeepTrio supports germline variant-calling in diploid organisms for the following types of input data:

Please also note:

How to run DeepVariant

We recommend using our Docker solution. The command will look like this:

BIN_VERSION="1.6.0"
docker run \
  -v "YOUR_INPUT_DIR":"/input" \
  -v "YOUR_OUTPUT_DIR:/output" \
  google/deepvariant:"${BIN_VERSION}" \
  /opt/deepvariant/bin/run_deepvariant \
  --model_type=WGS \ **Replace this string with exactly one of the following [WGS,WES,PACBIO,ONT_R104,HYBRID_PACBIO_ILLUMINA]**
  --ref=/input/YOUR_REF \
  --reads=/input/YOUR_BAM \
  --output_vcf=/output/YOUR_OUTPUT_VCF \
  --output_gvcf=/output/YOUR_OUTPUT_GVCF \
  --num_shards=$(nproc) \ **This will use all your cores to run make_examples. Feel free to change.**
  --logging_dir=/output/logs \ **Optional. This saves the log output for each stage separately.
  --haploid_contigs="chrX,chrY" \ **Optional. Heterozygous variants in these contigs will be re-genotyped as the most likely of reference or homozygous alternates. For a sample with karyotype XY, it should be set to "chrX,chrY" for GRCh38 and "X,Y" for GRCh37. For a sample with karyotype XX, this should not be used.
  --par_regions_bed="/input/GRCh3X_par.bed" \ **Optional. If --haploid_contigs is set, then this can be used to provide PAR regions to be excluded from genotype adjustment. Download links to this files are available in this page.
  --dry_run=false **Default is false. If set to true, commands will be printed out but not executed.

For details on X,Y support, please see DeepVariant haploid support and the case study in DeepVariant X, Y case study. You can download the PAR bed files from here: GRCh38_par.bed, GRCh37_par.bed.

To see all flags you can use, run: docker run google/deepvariant:"${BIN_VERSION}"

If you're using GPUs, or want to use Singularity instead, see Quick Start for more details or see all the setup options available.

For more information, also see:

How to cite

If you're using DeepVariant in your work, please cite:

A universal SNP and small-indel variant caller using deep neural networks. Nature Biotechnology 36, 983–987 (2018). <br/> Ryan Poplin, Pi-Chuan Chang, David Alexander, Scott Schwartz, Thomas Colthurst, Alexander Ku, Dan Newburger, Jojo Dijamco, Nam Nguyen, Pegah T. Afshar, Sam S. Gross, Lizzie Dorfman, Cory Y. McLean, and Mark A. DePristo.<br/> doi: https://doi.org/10.1038/nbt.4235

Additionally, if you are generating multi-sample calls using our DeepVariant and GLnexus Best Practices, please cite:

Accurate, scalable cohort variant calls using DeepVariant and GLnexus. Bioinformatics (2021).<br/> Taedong Yun, Helen Li, Pi-Chuan Chang, Michael F. Lin, Andrew Carroll, and Cory Y. McLean.<br/> doi: https://doi.org/10.1093/bioinformatics/btaa1081

Why Use DeepVariant?

<a name="myfootnote1">(1)</a>: Time estimates do not include mapping.

How DeepVariant works

Stages in DeepVariant

For more information on the pileup images and how to read them, please see the "Looking through DeepVariant's Eyes" blog post.

DeepVariant relies on Nucleus, a library of Python and C++ code for reading and writing data in common genomics file formats (like SAM and VCF) designed for painless integration with the TensorFlow machine learning framework. Nucleus was built with DeepVariant in mind and open-sourced separately so it can be used by anyone in the genomics research community for other projects. See this blog post on Using Nucleus and TensorFlow for DNA Sequencing Error Correction.

DeepVariant Setup

Prerequisites

Official Solutions

Below are the official solutions provided by the Genomics team in Google Health.

NameDescription
DockerThis is the recommended method.
Build from sourceDeepVariant comes with scripts to build it on Ubuntu 20.04. To build and run on other Unix-based systems, you will need to modify these scripts.
Prebuilt BinariesAvailable at gs://deepvariant/. These are compiled to use SSE4 and AVX instructions, so you will need a CPU (such as Intel Sandy Bridge) that supports them. You can check the /proc/cpuinfo file on your computer, which lists these features under "flags".

Contribution Guidelines

Please open a pull request if you wish to contribute to DeepVariant. Note, we have not set up the infrastructure to merge pull requests externally. If you agree, we will test and submit the changes internally and mention your contributions in our release notes. We apologize for any inconvenience.

If you have any difficulty using DeepVariant, feel free to open an issue. If you have general questions not specific to DeepVariant, we recommend that you post on a community discussion forum such as BioStars.

License

BSD-3-Clause license

Acknowledgements

DeepVariant happily makes use of many open source packages. We would like to specifically call out a few key ones:

We thank all of the developers and contributors to these packages for their work.

Disclaimer

This is not an official Google product.

NOTE: the content of this research code repository (i) is not intended to be a medical device; and (ii) is not intended for clinical use of any kind, including but not limited to diagnosis or prognosis.