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Bio Variant Calling Filtering Best Practices · freedomintelligence | DecimalAI

scienceby freedomintelligence

Bio Variant Calling Filtering Best Practices

freedomintelligence/bio-variant-calling-filtering-best-practices

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

Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and indels.

SkillScore91Maintained

Automatic

Data Engineer pack

Last verified 8/2/2026

What it changes

Passed 21 of 23 test cases with the skill, and 15 of 23 without it.

Without skill65%

With skill91%

Checks it passed that the model alone missed

Uses INFO/TLOD>6.3 in the filtering expression.
Uses np.min(depths) >= 10 to evaluate minimum depth across all samples.
Sets the threshold condition to F_MISSING<0.05 using the inclusion flag -i.

and 4 more in the full report

6 fixed15 passed either way2 still failing0 broke

Pass-rate lift: +26 pp
Tokens: +176%
Agent turns: 0%
Response time: -43%

Model gemini-3.6-flashMeasured 8/2/2026v121 of 23 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-variant-calling-filtering-best-practices/SKILL.md https://app.decimal.ai/s/freedomintelligence-bio-variant-calling-filtering-best-practices/SKILL.md

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

decimalai skills add freedomintelligence-bio-variant-calling-filtering-best-practices

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

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

Raw file: /s/freedomintelligence-bio-variant-calling-filtering-best-practices/SKILL.md ↗ · machine-readable summary at /s/freedomintelligence-bio-variant-calling-filtering-best-practices.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

I want to filter out variant sites in `input.vcf` where more than 5% of genotypes across all samples are missing using `bcftools filter`. What is the exact keyword metric and condition to enforce this?

What was checked, without and with the skill
Checked	Without skill	With skill
Uses the F_MISSING keyword metric in the filter expression.	Passed	Passed
Sets the threshold condition to F_MISSING<0.05 using the inclusion flag -i.	Missed	Passed

case-07 · 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.md351 linessingle file

Variant Filtering Best Practices

Filter Selection Decision Tree

Is dataset large enough for VQSR? (>30 exomes or WGS)
├── Yes → Use VQSR (machine learning)
└── No → Use hard filters
    ├── Germline → GATK recommended thresholds
    └── Somatic → Caller-specific filters + manual review

GATK Hard Filter Thresholds

# SNPs
gatk VariantFiltration \
    -R reference.fa \
    -V raw_snps.vcf \
    -O filtered_snps.vcf \
    --filter-expression "QD < 2.0" --filter-name "QD2" \
    --filter-expression "FS > 60.0" --filter-name "FS60" \
    --filter-expression "MQ < 40.0" --filter-name "MQ40" \
    --filter-expression "MQRankSum < -12.5" --filter-name "MQRankSum-12.5" \
    --filter-expression "ReadPosRankSum < -8.0" --filter-name "ReadPosRankSum-8" \
    --filter-expression "SOR > 3.0" --filter-name "SOR3"

Track record

Benchmark

21 / 23

test cases passed, vs 15 / 23 without

Adoption

Users: 4
Times used: 28

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/filtering-best-practices/SKILL.md

View on GitHub ↗

Imported 8/1/2026Version v1

Other skills for the same job

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bio-variant-calling-filtering-best-practicesComprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and indels. Use when filtering variants using GATK best practices.Close match+32 pp pass-rate lift

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