Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-longread-structural-variants

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

OpenClawNanoClawAnalysisReproductionbio-longread-structural-variants🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qcdetect

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-longread-structural-variants

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

CLI: sniffles --input aligned.bam --vcf svs.vcf, cuteSV aligned.bam ref.fa svs.vcf output/.
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/.
sniffles --input aligned.bam \ --vcf structural_variants.vcf \ --reference reference.fa \ --threads 4.

Source Doc

Excerpt From SKILL.md

Sniffles2 - Population Calling

Goal: Jointly call and genotype structural variants across a cohort of long-read samples for population-level SV analysis.

Approach: Generate per-sample SNF signature files from individual BAMs, then merge and jointly genotype all samples in a single Sniffles2 call.


## 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 \
    --vcf population_svs.vcf \
    --reference reference.fa

Use cases

Use when detecting deletions, insertions, inversions, translocations, or complex rearrangements from ONT or PacBio data, especially those missed by short-read methods.