DeepVariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Availability
DeepVariant is a suite of Python/C++ programs that run on any Unix-like operating system. For convenience the documentation refers to building and running DeepVariant on Google Cloud Platform, but the tools themselves can be built and run on any standard Linux computer, including on-premise machines. Pre-built binaries are available at gs://deepvariant/. Alternatively, see Building and testing DeepVariant for more information on building DeepVariant from sources for your platform.
Documentation
- DeepVariant release notes
- Building and testing DeepVariant
- DeepVariant quick start
- DeepVariant via Docker
- DeepVariant whole genome case study
- DeepVariant exome case study
- DeepVariant usage guide
- DeepVariant model training
About DeepVariant
For technical details describing how DeepVariant works please see our preprint.
Briefly, we started with some of the reference genomes from Genome in a Bottle, for which there is high-quality ground truth available (or the closest approximation currently possible). Using multiple replicates of these genomes, we produced approximately one hundred million training examples in the form of multi-channel tensors encoding the sequencing instrument data, and then trained a TensorFlow-based image classification model (inception-v3) to assign genotype likelihoods from the experimental data produced by the instrument. Read additional information on the Google Research blog.
Evaluating DeepVariant
We are delighted to see several external evaluations of the DeepVariant method.
The 2016 PrecisionFDA Truth Challenge, administered by the FDA, assessed several community-submitted variant callsets on the (at the time) blinded evaluation sample, HG002. DeepVariant won the Highest SNP Performance award in the challenge.
DNAnexus posted an extensive evaluation of several variant calling methods, including DeepVariant, using a variety of read sets from HG001, HG002, and HG005.
Support
The Genomics team in Google Brain actively supports DeepVariant and are always interested in improving the quality of DeepVariant. If you run into an issue, we recommend you follow one of two approaches to getting the issue resolved.
If you have found a bug in DeepVariant - i.e., the code itself needs to be fixed - please report the problem on our Issue tracker. Make sure to add enough detail to your report that we can reproduce the problem and fix it. We encourage including links to snippets of BAM/VCF/etc. files that provoke the bug, if possible. Depending on the severity of the issue we may patch DeepVariant immediately with the fix or roll it into the next release.
If you have general questions about DeepVariant usage, please post your question to BioStars, adding the tag 'deepvariant'. We monitor BioStars posts tagged with DeepVariant and will respond as needed there.
Contributing
Interested in contributing? See CONTRIBUTING.
License
DeepVariant is licensed under the terms of the BSD-3-Clause license.
Acknowledgements
DeepVariant happily makes use of many open source packages. We'd 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.