Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

deepvariant

Maintainer FreedomIntelligence · Last updated April 1, 2026

deepvariant.

OpenClawNanoClawAnalysisReproductiondeepvariantopenclaw medical skillsadditional scientific toolsbioinformatics-genomics

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/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

Docker (Recommended)

docker pull google/deepvariant:1.6.1

## Model Types

| Model | Data Type | Use Case |
|-------|-----------|----------|
| `WGS` | Illumina WGS | Whole genome sequencing |
| `WES` | Illumina WES | Whole exome/targeted |
| `PACBIO` | PacBio HiFi | Long-read HiFi |
| `ONT_R104` | ONT R10.4 | Oxford Nanopore |
| `HYBRID_PACBIO_ILLUMINA` | Mixed | Hybrid assemblies |

## Step-by-Step Workflow

For more control, run each step separately: