DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
DeepVariant-on-Spark is a germline short variant calling pipeline that runs Google DeepVariant on Apache Spark at scale.
Scalable and High Performance Variant Calling on Cluster Environments
Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated via Snakemake.
Notebooks and examples for DeepVariant on Spark project.
A Snakemake workflow for variant calling with DeepVariant, and optionally joint variant calling using GLnexus.
Workflows for whole-genome/exome sequencing data analysis
Comparative analysis of next-generation sequencing and genome assembly strategies in Pleurodeles waltl and related vertebrate genomes — MSc Bioinformatics NGS coursework
A small repo that eases use of google's deepvariant with GWA metastudies about hypertension
Germline variant calling pipeline
Showcase of DeepVariant variant calling with fine-tuning on small genomic datasets. Includes example scripts, notebook, and comparison of pretrained vs fine-tuned models.
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