Python-DeepVariantGoogle开源深度学习模型将基因组中的识别变异任务转换为图像分类问题的基因组学工具

# DeepVariant 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](https://github.com/google/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](https://www.tensorflow.org/) machine learning framework. ## Why Use DeepVariant? * **High accuracy** - In 2016 DeepVariant won [PrecisionFDA Truth Challenge](https://precision.fda.gov/challenges/truth/results) for best SNP Performance. DeepVariant maintains high accuracy across data from different sequencing technologies, prep methods, and species. * **Flexibility** - Out-of-the-box use for [PCR-positive](https://ai.googleblog.com/2018/04/deepvariant-accuracy-improvements-for.html) samples and [low quality sequencing runs](https://blog.dnanexus.com/2018-01-16-evaluating-the-performance-of-ngs-pipelines-on-noisy-wgs-data/), and easy adjustments for [different sequencing technologies](https://google.github.io/deepvariant/posts/2019-01-14-highly-accurate-snp-and-indel-calling-on-pacbio-ccs-with-deepvariant/) and [non-human species](https://google.github.io/deepvariant/posts/2018-12-05-improved-non-human-variant-calling-using-species-specific-deepvariant-models/). * **Ease of use** - No filtering is needed beyond setting your preferred minimum quality threshold. * **Cost effectiveness** - With an optimized setup on [Google Cloud](https://cloud.google.com/genomics/deepvariant), it costs ~$2-3 to call a whole genome and $0.20 to call an exome with preemptible instances. * **Speed** - On a 64-core CPU-only machine, DeepVariant completes a 50x WGS in 5 hours and an exome in 16 minutes [(1)](#myfootnote1)</sup>. Multiple options for acceleration exist, taking the WGS pipeline to as fast as 40 minutes (see [external solutions](#external-solutions)). * **Usage options** - DeepVariant can be run via Docker or binaries, using both on-premise hardware or in the cloud, with support for hardware accelerators like GPUs and TPUs. <a name="myfootnote1">(1)</a>: Time estimates do not include mapping. ## DeepVariant Setup ### Prerequisites * Unix-like operating system (cannot run on Windows) * Python 2.7 ### Official Solutions Below are the official solutions provided by the [Genomics team in Google Brain](https://research.google.com/teams/brain/genomics/). Name | Description :-------------------------------------------------------------------------------------------------: | ----------- [Docker](https://github.com/google/deepvariant/blob/r0.8/docs/deepvariant-quick-start.md) | This is the recommended method. [Build from source](https://github.com/google/deepvariant/blob/r0.8/docs/deepvariant-build-test.md) | 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/`](https://console.cloud.google.com/storage/browser/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". ### External Solutions The following pipelines are not created or maintained by the [Genomics team in Google Brain](https://research.google.com/teams/brain/genomics/). Please contact the relevant teams if you have any questions or concerns. Name | Description :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | ----------- [Running DeepVariant on Google Cloud Platform](https://cloud.google.com/genomics/docs/tutorials/deepvariant) | Docker-based pipelines optimized for cost and speed. Code can be found [here](https://github.com/googlegenomics/gcp-deepvariant-runner). [DeepVariant-on-spark from ATGENOMIX](https://github.com/atgenomix/deepvariant-on-spark) | 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](https://docs.parabricks.com/standalone-tools/deepvariant) | 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](https://platform.dnanexus.com/app/deepvariant_germline) | Offers parallelized execution with a GUI interface (requires platform account). [Nextflow Pipeline](https://github.com/nf-core/deepvariant) | Offers parallel processing of multiple BAMs and Docker support. [DNAstack Pipeline](https://app.dnastack.com/auth/realms/DNAstack/protocol/openid-connect/auth?client_id=dnastack-client&redirect_uri=https%3A%2F%2Fapp.dnastack.com%2F%3Fredirect_fragment%3D%252Forg%252F473079%252Fproj%252F473096%252Fapp%252Fworkflow%252F425685%252Frun&state=42231553-9fbc-4d71-a10e-d6ce42415c01&nonce=daf2568d-4fe7-48e2-ab60-858937244a87&response_mode=query&response_type=code&scope=openid) | Cost-optimized DeepVariant pipeline (requires platform account). ## Run DeepVariant * [DeepVariant Quickstart](https://github.com/google/deepvariant/blob/r0.8/docs/deepvariant