Detect large DNA changes, such as deletions, insertions, and inversions, from aligned ONT or PacBio long reads. Use command-line tools to produce variant files, combine samples or callers, and filter or annotate results.
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.
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See how to installReview the instructions the agent will receive before you install.
Reference examples tested with: bcftools 1.19+
Before using code patterns, verify installed versions match. If versions differ:
<tool> --version then <tool> --help to confirm flagsIf code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
"Call structural variants from my long reads" → Detect large deletions, insertions, inversions, duplications, and translocations with precise breakpoint resolution from ONT or PacBio alignments.
sniffles --input aligned.bam --vcf svs.vcf, cuteSV aligned.bam ref.fa svs.vcf output/# Call SVs from aligned BAM
sniffles --input aligned.bam \
--vcf structural_variants.vcf \
--reference reference.fa \
--threads 4
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
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
# cuteSV SV calling
cuteSV aligned.bam reference.fa output.vcf work_dir/ \
--threads 8 \
--min_support 3 \
--min_size 50 \
--genotype
# 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
# 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 for ONT data
svim alignment output_dir/ aligned.bam reference.fa \
--insertion_sequences \
--read_names \
--sample sample_name
# Discover signatures
pbsv discover aligned.bam signatures.svsig.gz
# Call SVs
pbsv call reference.fa signatures.svsig.gz structural_variants.vcf
# 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
# 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 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
| Type | Code | Description |
|---|---|---|
| Deletion | DEL | Sequence removed |
| Insertion | INS | Sequence added |
| Inversion | INV | Sequence inverted |
| Duplication | DUP | Sequence duplicated |
| Translocation | BND | Breakend (complex) |
| 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 |
| 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 | SV Detection |
|---|---|
| 5-10x | Large SVs (>1kb) |
| 10-20x | Most SVs |
| 20-30x | High confidence |
| >30x | Mosaic/rare SVs |
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