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Bio Gatk Variant Calling · freedomintelligence | DecimalAI

scienceby freedomintelligence

Bio Gatk Variant Calling

freedomintelligence/bio-gatk-variant-calling

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

Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality score recalibration (VQSR).

SkillScore100Maintained

Automatic

Research pack

Last verified 8/2/2026

What it changes

Passed 24 of 24 test cases with the skill, and 21 of 24 without it.

Without skill88%

With skill100%

Checks it passed that the model alone missed

Sets --truth-sensitivity-filter-level 99.5.
Runs gatk HaplotypeCaller followed by gatk GenotypeGVCFs.
Sets HapMap resource options as --resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap.vcf.gz.

3 fixed21 passed either way0 still failing0 broke

Pass-rate lift: +13 pp
Tokens: +233%
Agent turns: 0%
Response time: -50%

Model gemini-3.6-flashMeasured 8/2/2026v124 of 24 cases passed with skill

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-gatk-variant-calling/SKILL.md https://app.decimal.ai/s/freedomintelligence-bio-gatk-variant-calling/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add freedomintelligence-bio-gatk-variant-calling, 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-gatk-variant-calling/ and pins it in .decimal/skills.lock

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

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

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

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

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 3 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 3

Prompt

In the standard GATK VQSR workflow for human whole genome SNP filtering, what value should be passed to `--truth-sensitivity-filter-level` in `gatk ApplyVQSR`?

What was checked, without and with the skill
Checked	Without skill	With skill
Sets --truth-sensitivity-filter-level 99.5.	Missed	Passed

case-12 · 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.md387 linessingle file

GATK Variant Calling

GATK HaplotypeCaller is the gold standard for germline variant calling. This skill covers the GATK Best Practices workflow.

Prerequisites

BAM files should be preprocessed:

Mark duplicates
Base quality score recalibration (BQSR) - optional but recommended

Single-Sample Calling

Basic HaplotypeCaller

gatk HaplotypeCaller \
    -R reference.fa \
    -I sample.bam \
    -O sample.vcf.gz

With Standard Annotations

gatk HaplotypeCaller \
    -R reference.fa \
    -I sample.bam \

Track record

Benchmark

24 / 24

test cases passed, vs 21 / 24 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/gatk-variant-calling/SKILL.md

View on GitHub ↗

Imported 8/1/2026Version v1

Other skills for the same job

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bio-gatk-variant-callingVariant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality score recalibration (VQSR). Use when calling variants with GATK HaplotypeCaller.Close match+27 pp pass-rate lift

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