lobster-genomics 1.1.2

Genomics agent for Lobster AI (VCF, PLINK, GWAS, variant annotation)

lobster-genomics

Genomics analysis for VCF and PLINK data with GWAS, QC, and variant annotation capabilities.

Installation

pip install lobster-genomics

Agents

Agent	Description
genomics_expert	Full genomics workflow orchestration including data loading, quality control, GWAS analysis, and variant annotation.

Services

Service	Purpose
GWASService	Genome-wide association study analysis with linear/logistic regression
VariantAnnotationService	Variant functional annotation via Ensembl VEP integration
GenomicsQualityService	Comprehensive QC including call rate, MAF, HWE, and heterozygosity

Features

• Load VCF files (whole genome sequencing) and PLINK files (SNP arrays)
• Comprehensive quality control with configurable thresholds
• Call rate filtering at both sample and variant level
• Minor allele frequency (MAF) filtering for rare variant removal
• Hardy-Weinberg equilibrium testing for genotyping errors
• Heterozygosity outlier detection for sample quality assessment
• Linear and logistic regression GWAS with covariate support
• Lambda GC calculation for population stratification assessment
• Principal component analysis (PCA) for ancestry detection
• Variant functional annotation via Ensembl VEP API
• Manhattan plots and QQ plots for GWAS visualization
• PCA scatter plots colored by phenotype or ancestry

Requirements

• Python 3.12+
• lobster-ai >= 1.0.0
• cyvcf2 (VCF parsing)
• bed-reader (PLINK file support)
• sgkit (GWAS and PCA analysis)

Tier Requirement

This is a premium agent. Access is controlled at runtime via Lobster AI's tier system.

Documentation

Full documentation: docs.omics-os.com/docs/agents/genomics

License

MIT