Data & ReproClinical MedicineFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-variant-calling-deepvariant

Maintainer FreedomIntelligence · Last updated April 1, 2026

Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data. Use when calling variants with DeepVariant deep learning caller.

OpenClawNanoClawAnalysisReproductionbio-variant-calling-deepvariant🧬 bioinformatics (gptomics bio-* suite)bioinformatics — clinical databases & variant analysisdeep

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-calling-deepvariant

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

docker pull google/deepvariant:1.6.1-gpu.
for bam in *.bam; do sample=$(basename $bam.bam) docker run -v "${PWD}:/data" google/deepvariant:1.6.1 \ /opt/deepvariant/bin/run_deepvariant \ --model_type=WGS \ --ref=/data/reference.fa \ --reads=/data/$bam \ --output_vcf=/data/${sample}.vcf.gz \ --output_gvcf=/data/${sample}.g.vcf.gz \ --num_shards=16 done.

Source Doc

Excerpt From SKILL.md

Installation

Goal: Install DeepVariant via Docker or Singularity container.

Approach: Pull the pre-built container image matching the target platform (CPU or GPU).

Docker (Recommended)

docker pull google/deepvariant:1.6.1

## Basic Usage

**Goal:** Call germline variants from aligned reads using DeepVariant's deep learning model.

**Approach:** Run the all-in-one `run_deepvariant` wrapper specifying model type, reference, reads, and output paths.

**"Call variants with DeepVariant"** → Convert aligned read pileups into image tensors, classify with a CNN, and output genotyped VCF.