bio-variant-calling-structural-variant-calling
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-calling-structural-variant-calling --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: bcftools 1.19+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Structural Variant Calling (Short Reads) **"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` ## Manta (Recommended) ```bash # 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 ```bash # Somatic SV calling configManta.py \ --tumorBam tumor.bam \ --normalBam normal.bam \
- Version Compatibility
- Manta (Recommended)
- Manta Tumor-Normal Mode
- Manta Options
- Delly
- Delly Somatic Mode
- Delly SV Types
- LUMPY
- Smoove (LUMPY Wrapper)
- Merge Multiple Callers
- Filter SV Calls
- Annotate SVs
- SV Types
- Comparison: Manta vs Delly vs LUMPY
Configure Manta run (creates runWorkflow.py) configManta.py \ Execute manta_run/runWorkflow.py -j 8 Somatic SV calling manta_somatic/runWorkflow.py -j 8 Output includes: WES mode (for exome data) RNA-seq mode Call SVs
What does the bio-variant-calling-structural-variant-calling skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-calling-structural-variant-calling --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.