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DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. 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.
(1): Time estimates do not include mapping.
Below are the official solutions provided by the Genomics team in Google Brain.
| Name | Description |
|---|---|
| Docker | This is the recommended method. |
| Build from source | DeepVariant comes with scripts to build it on Ubuntu 14 and 16, with Ubuntu 16 recommended. To build and run on other Unix-based systems, you will need to modify these scripts. |
| Prebuilt Binaries | Available 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". |
The following pipelines are not created or maintained by the Genomics team in Google Brain. Please contact the relevant teams if you have any questions or concerns.
| Name | Description |
|---|---|
| Running DeepVariant on Google Cloud Platform | Docker-based pipelines optimized for cost and speed. Code can be found here. |
| DeepVariant-on-spark from ATGENOMIX | A germline short variant calling pipeline that runs DeepVariant on Apache Spark at scale with support for multi-GPU clusters (e.g. NVIDIA DGX-1). |
| Parabricks | An accelerated DeepVariant pipeline with multi-GPU support that runs our WGS pipeline in just 40 minutes, at a cost of $2-$3 per sample. This provides a 7.5x speedup over a 64-core CPU-only machine at lower cost. |
| DNAnexus DeepVariant App | Offers parallelized execution with a GUI interface (requires platform account). |
| Nextflow Pipeline | Offers parallel processing of multiple BAMs and Docker support. |
| DNAstack Pipeline | Cost-optimized DeepVariant pipeline (requires platform account). |
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.
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.
This is not an official Google product.
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