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Bio Variant Calling Deepvariant · freedomintelligence | DecimalAI

scienceby freedomintelligence

Bio Variant Calling Deepvariant

freedomintelligence/bio-variant-calling-deepvariant

Source FreedomIntelligence/OpenClaw-Medical-Skills ↗License Not recorded

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

SkillScore95Maintained

Automatic

Research pack

Last verified 8/2/2026

What it changes

Passed 19 of 20 test cases with the skill, and 13 of 20 without it.

Without skill64%

With skill95%

Checks it passed that the model alone missed

The model type specified is ONT_R104.
The GLnexus command sets --config to DeepVariantWGS.
The GLnexus config preset specified is DeepVariantWES.

and 6 more in the full report

8 fixed13 passed either way0 still failing1 broke

Pass-rate lift: +32 pp
Tokens: +116%
Agent turns: 0%
Response time: -54%

Model gemini-3.6-flashMeasured 8/2/2026v121 of 22 cases passed with skill · 20 comparable

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/freedomintelligence-bio-variant-calling-deepvariant/SKILL.md https://app.decimal.ai/s/freedomintelligence-bio-variant-calling-deepvariant/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add freedomintelligence-bio-variant-calling-deepvariant, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/freedomintelligence-bio-variant-calling-deepvariant/ and pins it in .decimal/skills.lock

decimalai skills add freedomintelligence-bio-variant-calling-deepvariant

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/freedomintelligence-bio-variant-calling-deepvariant/SKILL.md https://app.decimal.ai/s/freedomintelligence-bio-variant-calling-deepvariant/SKILL.md

Raw file: /s/freedomintelligence-bio-variant-calling-deepvariant/SKILL.md ↗ · machine-readable summary at /s/freedomintelligence-bio-variant-calling-deepvariant.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 6 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 6

Prompt

When performing joint genotyping on a multi-sample cohort of Illumina exome gVCFs using GLnexus in Docker, which `--config` preset must be passed to `glnexus_cli`?

What was checked, without and with the skill
Checked	Without skill	With skill
The GLnexus config preset specified is DeepVariantWES.	Missed	Passed

case-11 · gemini-3.6-flash · 8/2/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md268 linessingle file

DeepVariant Variant Calling

Installation

Docker (Recommended)

docker pull google/deepvariant:1.6.1

# Or with GPU support
docker pull google/deepvariant:1.6.1-gpu

Singularity

singularity pull docker://google/deepvariant:1.6.1

Basic Usage

One-Step Run (run_deepvariant)

docker run -v "${PWD}:/input" -v "${PWD}/output:/output" \
    google/deepvariant:1.6.1 \
    /opt/deepvariant/bin/run_deepvariant \

Track record

Benchmark

19 / 20

test cases passed, vs 13 / 20 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/1/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

FreedomIntelligence / OpenClaw-Medical-Skills

skills/variant-interpretation-acmg/bioSkills/deepvariant/SKILL.md

View on GitHub ↗

Imported 8/1/2026Version v1

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bio-variant-calling-deepvariantDeep 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.Close match+36 pp pass-rate lift

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