| 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
- Calculate: Prepare VCF indices and sequence mappings.
- Execute: Run haplotype graph resolution algorithms.
- Assess: Perform switch error evaluation and quality flagging.
- Generate: Output structured phased VCF representation.
- 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 VCFsannotation — Downstream annotation of phased haplotypes
Citations
