master2pgsnp

master2pgsnp converts variant data from MasterVar format to pgSnp format to enable integration with genomic browsers and downstream phenotype association and interval operations.

Key Features:

• Format Conversion: Converts variant records from the MasterVar format into pgSnp format.
• Browser Compatibility: Produces pgSnp output compatible with genomic browsers for visualization and interpretation of genetic variants.
• Integration with Analysis Tools: Generates outputs suitable for phenotype association analyses and interval operations.
• Galaxy Integration: Interfaces with Galaxy via its API or the Bioblend library to support execution within Galaxy-based workflows on the Institut Pasteur cluster.

Scientific Applications:

• Variant data standardization: Standardizes variant representation to enable downstream comparative analyses and tool interoperability.
• Phenotype association studies: Provides pgSnp-formatted data for use in phenotype association analyses and interval-based genomic queries.
• Computational biomedical research: Supports reproducible workflows executed through Galaxy on the Institut Pasteur cluster.

Methodology:

Uses Galaxy as an execution engine and interfaces with Galaxy through its API or the Bioblend library to perform conversion and execute workflows on the Institut Pasteur cluster.