genomics-phasing

name	genomics-phasing
description	Haplotype phasing analysis: phase block N50, phased fraction, PS (Phase Set) field parsing, pipe-delimited genotype detection. Wraps WhatsHap, SHAPEIT5, Eagle2.
version	0.2.0
author	OmicsClaw
license	MIT
tags	["genomics","phasing","haplotype","WhatsHap","SHAPEIT"]
metadata	{"omicsclaw":{"domain":"genomics","emoji":"🔀","trigger_keywords":["haplotype phasing","WhatsHap","SHAPEIT","Eagle","phasing"],"allowed_extra_flags":["--method"],"legacy_aliases":["phase"],"saves_h5ad":false}}

🔀 Haplotype Phasing

Haplotype phasing for variant data. Wraps WhatsHap, SHAPEIT, and Eagle.

CLI Reference

python omicsclaw.py run genomics-phasing --demo
python omicsclaw.py run genomics-phasing --input <data.vcf> --output <dir>

Why This Exists

• Without it: Variants remain independent loci without knowledge of allelic connectivity
• With it: Haplotypes are formed spanning genes, essential for compound heterozygote analysis
• Why OmicsClaw: Standardizes input and output across read-backed and population-backed phasing tools

Workflow

1. Calculate: Prepare VCF indices and sequence mappings.
2. Execute: Run haplotype graph resolution algorithms.
3. Assess: Perform switch error evaluation and quality flagging.
4. Generate: Output structured phased VCF representation.
5. Report: Synthesize N50 phase block stats into tables.

Example Queries

• "Phase this vcf file using WhatsHap"
• "Use SHAPEIT for population phasing of variants"

Output Structure

output_directory/
├── report.md
├── result.json
├── phased.vcf.gz
├── figures/
│   └── phase_block_distribution.png
├── tables/
│   └── phasing_metrics.csv
└── reproducibility/
    ├── commands.sh
    ├── requirements.txt
    └── checksums.sha256

Safety

• Local-first: Strict offline processing without external upload.
• Disclaimer: Requires OmicsClaw reporting structures and disclaimers.
• Audit trail: Hyperparameters and operational flow states are logged fully.

Integration with Orchestrator

Trigger conditions:

• Automatically invoked dynamically based on tool metadata and user intent matching.

Chaining partners:

• variant-call — Upstream generation of raw VCFs
• annotation — Downstream annotation of phased haplotypes

Citations

• WhatsHap
• SHAPEIT