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bio-variant-calling-structural-variant-calling
Maintainer FreedomIntelligence · Last updated April 1, 2026
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. Use when detecting structural variants from short-read data.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-calling-structural-variant-calling
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: configManta.py (Manta), delly call, lumpyexpress/smoove call.
- Call structural variants from my WGS data" → Detect large genomic rearrangements (deletions, insertions, inversions, duplications, translocations) using split-read and discordant-pair evidence. CLI: configManta.py (Manta), delly call, lumpyexpress/smoove call.
- configManta.py \ --bam sample.bam \ --referenceFasta reference.fa \ --runDir manta_run.
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 when detecting structural variants from short-read data.
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
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