Ready to supercharge your AI agents?

Install any skill in seconds. Free to start, no credit card required.

Bio Variant Calling Structural Variant Calling · freedomintelligence | DecimalAI

scienceby freedomintelligence

Bio Variant Calling Structural Variant Calling

freedomintelligence/bio-variant-calling-structural-variant-calling

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

Call structural variants (SVs) from short-read sequencing using Manta, Delly, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations that are too large for standard SNV callers.

SkillScore86Maintained

Automatic

Research pack

Last verified 8/3/2026

What it changes

Passed 18 of 21 test cases with the skill, and 15 of 21 without it.

Without skill73%

With skill86%

Checks it passed that the model alone missed

Identifies BND as the code for translocations
Includes parameters --fasta, --outdir, and -p 8
States that 10x coverage detects large SVs greater than 1kb

and 1 more in the full report

4 fixed15 passed either way2 still failing1 broke

Pass-rate lift: +14 pp
Tokens: +86%
Agent turns: 0%
Response time: -15%

Model gemini-3.6-flashMeasured 8/3/2026v119 of 22 cases passed with skill · 21 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-structural-varian-de2d40/SKILL.md https://app.decimal.ai/s/freedomintelligence-bio-variant-calling-structural-variant-calling/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add freedomintelligence-bio-variant-calling-structural-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-variant-calling-structural-varian-de2d40/ and pins it in .decimal/skills.lock

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

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

curl -fsSL --create-dirs -o .claude/skills/freedomintelligence-bio-variant-calling-structural-varian-de2d40/SKILL.md https://app.decimal.ai/s/freedomintelligence-bio-variant-calling-structural-variant-calling/SKILL.md

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

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 4 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 4

Prompt

In VCF specifications for structural variants, what are the five standard 3-letter or abbreviated code identifiers used in `SVTYPE` tags for deletions, insertions, inversions, duplications, and inter-chromosomal breakends?

What was checked, without and with the skill
Checked	Without skill	With skill
Identifies BND as the code for translocations	Missed	Passed
Lists DEL, INS, INV, DUP as structural variant type codes	Passed	Passed

case-19 · gemini-3.6-flash · 8/3/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md245 linessingle file

Structural Variant Calling (Short Reads)

Manta (Recommended)

# Configure Manta run (creates runWorkflow.py)
configManta.py \
    --bam sample.bam \
    --referenceFasta reference.fa \
    --runDir manta_run

# Execute
manta_run/runWorkflow.py -j 8

# Output: manta_run/results/variants/
# - diploidSV.vcf.gz (germline SVs)
# - candidateSV.vcf.gz (all candidates)
# - candidateSmallIndels.vcf.gz (small indels)

Manta Tumor-Normal Mode

# Somatic SV calling
configManta.py \
    --tumorBam tumor.bam \
    --normalBam normal.bam \

Track record

Benchmark

18 / 21

test cases passed, vs 15 / 21 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/structural-variant-calling/SKILL.md

View on GitHub ↗

Imported 8/1/2026Version v1

Other skills for the same job

Published skills whose descriptions closely match this one, with their headline benchmark lift.

bio-variant-calling-structural-variant-callingCall structural variants (SVs) from short-read sequencing using Manta, Delly, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations that are too large for standard SNV callers. Use when detecting structural variants from short-read data.Close match+5 pp pass-rate lift

More skills from the same source and nearby in the registry, with their headline benchmark lift.