DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

PEPPER-Margin-DeepVariant

Deep Variant as a Nextflow pipeline

DeepVariant-on-Spark is a germline short variant calling pipeline that runs Google DeepVariant on Apache Spark at scale.

dv-trio provides a pipeline to call variants for a trio (father-mother-child) using DeepVariants [1]. Genomic Variant Calling Files (gVCFs) created by DeepVariants are then co_called together using GATK[2]. The resultant trio VCF is then post-processing with FamSeq[3] to eliminate mendelian errors.

WDL workflow for population variant calling using htsget, DeepVariant, and GLnexus

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.

Whole genome sequencing analysis pipeline for consumer hardware. 100% local, Docker-powered, free and open source.

No description available

No description available

No description available

call variants with deepvariant

A Nextflow pipeline for Google's DeepVariant

Notebooks and examples for DeepVariant on Spark project.

DeepVariant for Linux ARM64 (Graviton, Ampere, RK3588, Jetson) with hardware-accelerated inference via ONNX Runtime + ACL. Open-source variant calling on cheap ARM cloud and edge hardware.

A Pipeline for comparing GATK and Deepvariant

A Snakemake workflow for variant calling with DeepVariant, and optionally joint variant calling using GLnexus.

MGI train model

This repository is for hosting Jupyter notebooks for examining a couple of internal processes in DeepVariant

Repository for running deepvariant on K8s

Synthetic somatic mutation read-generation, variant calling pipelines (DeepVariant & GATK), and benchmarking framework for bioinformatics research.

Workflows for whole-genome/exome sequencing data analysis

This repository contains a docker container that runs DeepVariant on the Google Cloud Platform.

Implementation of Google Variant Caller -

DeepVariant implementation using PyTorch

Deepvariant edited bam/samtools aligned bam to vcf.gz with annotation and summary using snpEff

No description available

A snakemake workflow that calls variants from multi-sample illumina reads using Deepvariant and GLnexus

Benchmarking parabricks GPU-accelerated tools for GATK and beyond!