ArticleComputational and mathematical methods in medicine2020
DeepVariant-on-Spark: Small-Scale Genome Analysis Using a Cloud-Based Computing Framework.
Article in Computational and mathematical methods in medicine, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
9 citing papers in PubMed.
- AI-powered mapping of tumor immunity for optimized mRNA vaccine engineering.Frontiers in oncology · 2026Review
- The Role of Artificial Intelligence in Herpesvirus Detection, Transmission, and Predictive Modeling: With a Special Focus on Marek's Disease Virus.Pathogens (Basel, Switzerland) · 2025Review
- Development of a Japanese polygenic risk score model for amyloid-β PET imaging in Alzheimer's disease.Alzheimer's research & therapy · 2025Article
- Artificial intelligence in variant calling: a review.Frontiers in bioinformatics · 2025Review
- Performance analysis of conventional and AI-based variant callers using short and long reads.BMC bioinformatics · 2023Article
- Framing Apache Spark in life sciences.Heliyon · 2023Review
- Using Recurrent Neural Networks for Predicting Type-2 Diabetes from Genomic and Tabular Data.Diagnostics (Basel, Switzerland) · 2022Article
- Artificial intelligence applied in neoantigen identification facilitates personalized cancer immunotherapy.Frontiers in oncology · 2022Review
- OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow.BMC bioinformatics · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although sequencing a human genome has become affordable, identifying genetic variants from whole-genome sequence data is still a hurdle for researchers without adequate computing equipment or bioinformatics support. GATK is a gold standard method for the identification of genetic variants and has been widely used in genome projects and population genetic studies for many years. This was until the Google Brain team developed a new method, DeepVariant, which utilizes deep neural networks to construct an image classification model to identify genetic variants. However, the superior accuracy of DeepVariant comes at the cost of computational intensity, largely constraining its applications. Accordingly, we present DeepVariant-on-Spark to optimize resource allocation, enable multi-GPU support, and accelerate the processing of the DeepVariant pipeline. To make DeepVariant-on-Spark more accessible to everyone, we have deployed the DeepVariant-on-Spark to the Google Cloud Platform (GCP). Users can deploy DeepVariant-on-Spark on the GCP following our instruction within 20 minutes and start to analyze at least ten whole-genome sequencing datasets using free credits provided by the GCP. DeepVaraint-on-Spark is freely available for small-scale genome analysis using a cloud-based computing framework, which is suitable for pilot testing or preliminary study, while reserving the flexibility and scalability for large-scale sequencing projects.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.