bio-longread-structural-variants
Detect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM. Use when detecting deletions, insertions, inversions, translocations, or complex rearrangements from ONT or PacBio data, especially those missed by short-read methods.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-longread-structural-variants --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+ 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 Detection **"Call structural variants from my long reads"** → Detect large deletions, insertions, inversions, duplications, and translocations with precise breakpoint resolution from ONT or PacBio alignments. - CLI: `sniffles --input aligned.bam --vcf svs.vcf`, `cuteSV aligned.bam ref.fa svs.vcf output/` ## Sniffles2 - Basic SV Calling ```bash # Call SVs from aligned BAM sniffles --input aligned.bam \ --vcf structural_variants.vcf \ --reference reference.fa \ --threads 4 ``` ## Sniffles2 - Common Options ```bash sniffles --input aligned.bam \ --vcf structural_variants.vcf \ --reference reference.fa \ --threads 8 \ --minsupport 3 \ # Min supporting reads --minsvlen 50 \ # Min SV length --mapq 20 \ # Min mapping quality --output-rnames \ # Include read names --mosaic # Detect mosaic SVs ``` ##
- Version Compatibility
- Sniffles2 - Basic SV Calling
- Sniffles2 - Common Options
- Sniffles2 - Population Calling
- cuteSV - Alternative Caller
- cuteSV - ONT Optimized
- cuteSV - PacBio HiFi Optimized
- SVIM - Another Alternative
- pbsv - PacBio Specific
- Filter SV Calls
- Merge Multiple Callers
- Annotate SVs
- SV Types
- Key Parameters - Sniffles2
Call SVs from aligned BAM sniffles --input aligned.bam \ Step 1: Call SVs per sample with SNF output sniffles --input sample1.bam --snf sample1.snf --reference reference.fa sniffles --input sample2.bam --snf sample2.snf --reference reference.fa Step 2: Merge and genotype sniffles --input sample1.snf sample2.snf \ cuteSV SV calling cuteSV aligned.bam reference.fa output.vcf work_dir/ \ Settings optimized for ONT
What does the bio-longread-structural-variants skill do?
Detect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM. Use when detecting deletions, insertions, inversions, translocations, or complex rearrangements from ONT or PacBio data, especially those missed by short-read methods.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-longread-structural-variants --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.