Agent skill

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.

View SKILL.md on GitHub Repository
Stars 2,009
Forks 275

Install this agent skill to your Project

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

SKILL.md

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

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.

bash
# 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

cuteSV - Alternative Caller

bash
# cuteSV SV calling
cuteSV aligned.bam reference.fa output.vcf work_dir/ \
    --threads 8 \
    --min_support 3 \
    --min_size 50 \
    --genotype

cuteSV - ONT Optimized

bash
# Settings optimized for ONT
cuteSV aligned.bam reference.fa output.vcf work_dir/ \
    --threads 8 \
    --max_cluster_bias_INS 100 \
    --diff_ratio_merging_INS 0.3 \
    --max_cluster_bias_DEL 100 \
    --diff_ratio_merging_DEL 0.3 \
    --genotype

cuteSV - PacBio HiFi Optimized

bash
# Settings optimized for HiFi
cuteSV aligned.bam reference.fa output.vcf work_dir/ \
    --threads 8 \
    --max_cluster_bias_INS 1000 \
    --diff_ratio_merging_INS 0.9 \
    --max_cluster_bias_DEL 1000 \
    --diff_ratio_merging_DEL 0.5 \
    --genotype

SVIM - Another Alternative

bash
# SVIM for ONT data
svim alignment output_dir/ aligned.bam reference.fa \
    --insertion_sequences \
    --read_names \
    --sample sample_name

pbsv - PacBio Specific

bash
# Discover signatures
pbsv discover aligned.bam signatures.svsig.gz

# Call SVs
pbsv call reference.fa signatures.svsig.gz structural_variants.vcf

Filter SV Calls

bash
# Filter by quality and size
bcftools filter -i 'QUAL>=20 && ABS(SVLEN)>=50' svs.vcf > svs.filtered.vcf

# Keep only PASS
bcftools view -f PASS svs.vcf > svs.pass.vcf

# Filter specific SV types
bcftools view -i 'SVTYPE="DEL"' svs.vcf > deletions.vcf
bcftools view -i 'SVTYPE="INS"' svs.vcf > insertions.vcf

Merge Multiple Callers

bash
# Use SURVIVOR to merge SV callsets
SURVIVOR merge sample_files.txt 1000 2 1 1 0 50 merged_svs.vcf

# sample_files.txt contains VCF paths, one per line
# Parameters: max_distance, min_callers, type_agree, strand_agree, est_distance, min_size

Annotate SVs

bash
# Annotate with AnnotSV
AnnotSV -SVinputFile svs.vcf \
    -genomeBuild GRCh38 \
    -outputFile annotated_svs

# Or with bcftools
bcftools annotate -a gnomad_sv.vcf.gz -c INFO svs.vcf > svs.annotated.vcf

SV Types

Type Code Description
Deletion DEL Sequence removed
Insertion INS Sequence added
Inversion INV Sequence inverted
Duplication DUP Sequence duplicated
Translocation BND Breakend (complex)

Key Parameters - Sniffles2

Parameter Default Description
--minsupport auto Min supporting reads
--minsvlen 50 Min SV length
--mapq 20 Min mapping quality
--reference none Reference (for INS sequences)
--tandem-repeats none BED of tandem repeats
--mosaic off Detect mosaic SVs

Key Parameters - cuteSV

Parameter Default Description
--min_support 10 Min supporting reads
--min_size 30 Min SV length
--max_size 100000 Max SV length
--genotype off Output genotypes
--report_readid off Report read IDs

Coverage Guidelines

Coverage SV Detection
5-10x Large SVs (>1kb)
10-20x Most SVs
20-30x High confidence
>30x Mosaic/rare SVs

Related Skills

  • long-read-alignment - Generate input BAM
  • medaka-polishing - Polish assembly with SVs
  • variant-calling/structural-variant-calling - Short-read SV comparison

Recommended Agent Skills

Expand your agent's capabilities with these related and highly-rated skills.

FreedomIntelligence/OpenClaw-Medical-Skills

vcf-annotator

Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.

2,009 275
Explore
FreedomIntelligence/OpenClaw-Medical-Skills

chemist-analyst

Analyzes events through chemistry lens using molecular structure, reaction mechanisms, thermodynamics, kinetics, and analytical techniques (spectroscopy, chromatography, mass spectrometry). Provides insights on chemical processes, material properties, reaction pathways, synthesis, and analytical methods. Use when: Chemical reactions, material analysis, synthesis planning, process optimization, environmental chemistry. Evaluates: Molecular structure, reaction mechanisms, yield, selectivity, safety, environmental impact.

2,009 275
Explore
FreedomIntelligence/OpenClaw-Medical-Skills

bio-alignment-io

Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.

2,009 275
Explore
FreedomIntelligence/OpenClaw-Medical-Skills

sleep-analyzer

分析睡眠数据、识别睡眠模式、评估睡眠质量，并提供个性化睡眠改善建议。支持与其他健康数据的关联分析。

2,009 275
Explore
FreedomIntelligence/OpenClaw-Medical-Skills

metabolomics-workbench-database

Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.

2,009 275
Explore
FreedomIntelligence/OpenClaw-Medical-Skills

bio-hi-c-analysis-matrix-operations

Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expected matrices. Use when normalizing or transforming Hi-C matrices.

2,009 275
Explore

Didn't find tool you were looking for?

Be as detailed as possible for better results