convert2annovar

convert2annovar converts genotype calling formats into ANNOVAR-compatible input to enable downstream variant annotation and functional interpretation.

Key Features:

• Format Conversion: Translates multiple genotype calling formats into the ANNOVAR input format for variant annotation.
• ANNOVAR Compatibility: Produces outputs tailored for ANNOVAR to support downstream functional prediction and annotation workflows.
• Galaxy Integration: Executes within the Galaxy platform to integrate conversion steps into reproducible computational workflows.
• API-driven Execution: Uses the Galaxy API and the Bioblend library to communicate with and submit jobs for execution on the Institut Pasteur cluster.

Scientific Applications:

• Variant Annotation: Enables use of ANNOVAR for functional annotation of genetic variants.
• Disease Association Studies: Facilitates preparation of genotype data for analyses linking variants to disease phenotypes.
• Population Genetics and Evolutionary Biology: Supports analyses requiring variant annotations in population genetics and evolutionary studies.
• Personalized Medicine: Supports workflows that require variant annotation for clinical or precision medicine analyses.

Methodology:

Runs within the Galaxy framework, converting genotype calling formats to ANNOVAR format and using the Galaxy API with the Bioblend library to submit and manage jobs on the Institut Pasteur cluster.