bio-variant-calling-deepvariant
Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data.
npx skills add majiayu000/claude-skill-registry --skill deepvariant --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# DeepVariant Variant Calling ## Installation ### Docker (Recommended) ```bash docker pull google/deepvariant:1.6.0 # Or with GPU support docker pull google/deepvariant:1.6.0-gpu ``` ### Singularity ```bash singularity pull docker://google/deepvariant:1.6.0 ``` ## Basic Usage ### One-Step Run (run_deepvariant) ```bash docker run -v "${PWD}:/input" -v "${PWD}/output:/output" \ google/deepvariant:1.6.0 \ /opt/deepvariant/bin/run_deepvariant \ --model_type=WGS \ --ref=/input/reference.fa \ --reads=/input/sample.bam \ --output_vcf=/output/sample.vcf.gz \ --output_gvcf=/output/sample.g.vcf.gz \ --num_shards=16 ``` ### 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: ### Step 1: Make Examples ```bash docker run -v "${PWD}:/data" google/deepvariant:1.6.0 \ /opt/deepvariant/bin/make_examples \ --mode calling \ --ref /data/reference.fa \ --reads /data/sa
- Installation
- Docker (Recommended)
- Singularity
- Basic Usage
- One-Step Run (rundeepvariant)
- Model Types
- Step-by-Step Workflow
- Step 1: Make Examples
- Step 2: Call Variants
- Step 3: Postprocess Variants
- GPU Acceleration
- PacBio HiFi Calling
- ONT Calling
- Exome/Targeted Sequencing
docker pull google/deepvariant:1.6.0
Or with GPU support
docker pull google/deepvariant:1.6.0-gpu
singularity pull docker://google/deepvariant:1.6.0
docker run -v "${PWD}:/input" -v "${PWD}/output:/output" \
docker run -v "${PWD}:/data" google/deepvariant:1.6.0 \
docker run --gpus all -v "${PWD}:/data" \
Generate gVCFs for each sample
for bam in *.bam; do
doneWhat does the bio-variant-calling-deepvariant skill do?
Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill deepvariant --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.