longread-structural-variants

name	longread-structural-variants
description	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.
tool_type	cli
primary_tool	sniffles

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

# Call SVs from aligned BAM
sniffles --input aligned.bam \
    --vcf structural_variants.vcf \
    --reference reference.fa \
    --threads 4

Sniffles2 - Common Options

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.

# 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

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

cuteSV - ONT Optimized

# 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

# 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

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

pbsv - PacBio Specific

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

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

Filter SV Calls

# 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

# 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

# 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