<!-- # COPYRIGHT NOTICE # This file is part of the "Universal Biomedical Skills" project. # Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu> # All Rights Reserved. # # This code is proprietary and confidential. # Unauthorized copying of this file, via any medium is strictly prohibited. # # Provenance: Authenticated by MD BABU MIA -->

---

name: bio-genomics-phasing description: 'Haplotype phasing analysis: phase block N50, phased fraction, PS (Phase Set) field parsing, pipe-delimited genotype detection. Wraps WhatsHap, SHAPEIT5, Eagle2.' tool_type: mixed primary_tool: genomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools:

• read_file
• run_shell_command

---

🔀 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
    ├── environment.yml
    └── 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

<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->