Version Compatibility

Reference examples tested with: DeepVariant 1.6+, Entrez Direct 21.0+, bcftools 1.19+, minimap2 2.26+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• 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.

Clair3 Variant Calling

"Call variants from my long-read data" → Use deep learning to identify germline SNPs and small indels from ONT or PacBio aligned reads with high accuracy.

• CLI: run_clair3.sh --bam_fn=sample.bam --ref_fn=ref.fa --platform=ont

Basic Usage