AG
Data & Repro
agent-browser
Browse the web for any task — research topics, read articles, interact with web apps, fill forms, take screenshots, extract data, and test w…
FreedomIntelligence/OpenClaw-Medical-SkillsView
Data & Repro
ST
structural-variant-calling
Maintainer FreedomIntelligence · Last updated April 1, 2026
structural-variant-calling.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/structural-variant-calling
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- configManta.py \ --bam sample.bam \ --referenceFasta reference.fa \ --runDir manta_run.
- manta_run/runWorkflow.py -j 8.
Source Doc
Excerpt From SKILL.md
Somatic SV calling
configManta.py
--tumorBam tumor.bam
--normalBam normal.bam
--referenceFasta reference.fa
--runDir manta_somatic
manta_somatic/runWorkflow.py -j 8
WES mode (for exome data)
configManta.py
--bam sample.bam
--referenceFasta reference.fa
--exome \ # Use exome settings
--callRegions regions.bed.gz \ # Restrict to regions
--runDir manta_exome
RNA-seq mode
configManta.py
--bam rnaseq.bam
--referenceFasta reference.fa
--rna \ # RNA-seq mode
--runDir manta_rna
Use cases
- Use structural-variant-calling for genomics and bioinformatics workflows.
- Apply structural-variant-calling to sequencing, variant, or omics analysis tasks.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- long-read-sequencing/structural-variants - Long-read SV calling
- copy-number/cnvkit-analysis - Copy number variants
- variant-calling/filtering-best-practices - Filter VCF files
- alignment-files/alignment-filtering - Prepare BAM files
Related skills
Related skills
AL
Data & Repro
alpha-vantage
Access 20+ years of global financial data: equities, options, forex, crypto, commodities, economic indicators, and 50+ technical indicators.
K-Dense-AI/claude-scientific-skillsView
BI
Data & Repro
bio-alignment-filtering
Filter alignments by flag, quality, region, or paired status.
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Data & Repro
bio-alignment-indexing
Index BAM/CRAM files with samtools index for random access.
FreedomIntelligence/OpenClaw-Medical-SkillsView