bio-variant-calling-deepvariant

npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-calling-deepvariant --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

## Version Compatibility Reference examples tested with: GATK 4.5+, bcftools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # DeepVariant Variant Calling ## 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) ```bash docker pull google/deepvariant:1.6.1 # Or with GPU support docker pull google/deepvariant:1.6.1-gpu ``` ### Singularity ```bash singularity pull docker://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. ### One-Step Run (run_deepvaria

docker pull google/deepvariant:1.6.1
Or with GPU support
docker pull google/deepvariant:1.6.1-gpu
singularity pull docker://google/deepvariant:1.6.1
docker run -v "${PWD}:/input" -v "${PWD}/output:/output" \
docker run -v "${PWD}:/data" google/deepvariant:1.6.1 \
docker run --gpus all -v "${PWD}:/data" \
Generate gVCFs for each sample
for bam in *.bam; do
done