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