pantree-usage

name	pantree-usage
description	Run, debug, or explain Pantree analyses, CLI commands, Python APIs, scientific concepts, and GFA/VCF contracts. Use for gfa2vcf conversion, graph simplification, haplotype consolidation, reference-tree behavior, genotype interpretation, or Pantree file formats.

Pantree usage

Start by inspecting the installed command surface:

uv run pantree --help
uv run pantree <command> --help

Select the relevant reference:

• Read references/concepts.md before explaining or changing reference-tree, variant, coordinate, genotype, or consolidation behavior.
• Read references/gfa2vcf.md for graph-to-VCF commands and option selection.
• Read references/simplify.md for simplification and origin-metadata behavior.
• Read references/consolidate.md for single-haplotype consolidation.
• Read references/file-formats.md before changing or relying on GFA, VCF, compression, or provenance contracts.

Prefer small fixtures in tests/data/ for verification. Check that a fixture is present and non-empty. Preserve user data and never overwrite an input GFA or VCF with generated output.