数据与复现生物信息与基因组学FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-longread-structural-variants

维护者 FreedomIntelligence · 最近更新 2026年4月1日

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.

OpenClawNanoClaw分析处理复现实验bio-longread-structural-variants🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qcdetect

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

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

维护者: FreedomIntelligence
许可: MIT
最近更新: 2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

CLI：sniffles --input aligned.bam --vcf svs.vcf，cuteSV aligned.bam ref.fa svs.vcf output/。
Call structural variants ，面向 my long reads" → Detect large deletions，insertions，inversions，duplications，、 translocations ，支持 precise breakpoint resolution ，面向 ONT 或 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。

原始文档

SKILL.md 摘录

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

适用场景

适合在detecting deletions，insertions，inversions，translocations，或 complex rearrangements ，面向 ONT 或 PacBio data，especially those missed by short-read methods时使用。