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genomics-phasing

Phase variant data into haplotypes and generate phased VCF files.

155|26|Updated Mar 14, 2026
Search Tags:#genomics#variant analysis#vcf#phasing#haplotype#WhatsHap#SHAPEIT
One-click install
npx skills add https://github.com/TianGzlab/OmicsClaw --skill genomics-phasing
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: genomics-phasing
Source: https://github.com/TianGzlab/OmicsClaw/tree/main/skills/genomics/genomics-phasing
Command: npx skills add https://github.com/TianGzlab/OmicsClaw --skill genomics-phasing

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires numpy, pandas, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill addresses the challenge of understanding genetic variation by determining the specific combinations of alleles (haplotypes) that are inherited together on each chromosome. Without phasing, variants are treated as independent, hindering the analysis of complex genetic traits and disease associations.

Core Features & Use Cases

  • Haplotype Determination: Accurately phases variants using established tools like WhatsHap, SHAPEIT5, and Eagle2.
  • Quality Metrics: Computes essential phasing statistics such as phase block N50, fraction of phased heterozygous variants, and switch error rates.
  • Use Case: For a researcher studying a genetic disorder, phasing variants is crucial to identify compound heterozygous mutations, where two different deleterious alleles on the same gene are inherited, which might be missed with unphased data.

Quick Start

Use the genomics-phasing skill to phase the variants in the file 'my_variants.vcf'.

Frequently Asked Questions about genomics-phasing

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I phase variants in a VCF file to identify compound heterozygous mutations?▼

To phase variants in a VCF file, this analysis wraps WhatsHap, SHAPEIT5, and Eagle2 to determine allele combinations on chromosomes. It generates phased VCF files essential for identifying compound heterozygous mutations inherited on the same gene.

What is haplotype phasing and when do I need it for variant analysis?▼

Haplotype phasing determines specific combinations of alleles inherited together on each chromosome. You need variant phasing when analyzing complex genetic traits and disease associations, as unphased data treats variants independently and misses allelic linkage across loci.

Can I use WhatsHap and SHAPEIT5 for haplotype determination on my genomic data?▼

Yes, WhatsHap and SHAPEIT5 are integrated alongside Eagle2 for haplotype determination. You can use these established tools to process your variant data and produce phased VCF files for downstream analyses requiring allelic linkage knowledge.

How to calculate phase block N50 and switch error rates from phased VCF files?▼

Calculate phase block N50 and switch error rates by running haplotype phasing on your variant data. The process automatically computes these quality metrics, plus the fraction of phased heterozygous variants, to evaluate phasing continuity and accuracy.

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