DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
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.
A Snakemake workflow for variant calling with DeepVariant, and optionally joint variant calling using GLnexus.
Benchmarking parabricks GPU-accelerated tools for GATK and beyond!
Self-built GPU-accelerated WGS pipeline (NVIDIA Parabricks fq2bam + DeepVariant). Runs on a laptop GPU via Docker or a multi-GPU cluster via rootless Podman. hg38 + T2T, checkpoint-resume.
Germline variant calling pipeline
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