gatk_variant_select

gatk_variant_select extracts and selects genetic variants from Variant Call Format (VCF) files for targeted genomic analyses.

Key Features:

• Sample Extraction: Selects one or more samples from a VCF by complete sample names or pattern matching.
• Variant Filtering: Filters variants based on user-defined criteria within the VCF.
• Integration with Galaxy Platform: Executes variant selection workflows within the Galaxy platform as an execution engine, with execution on computational clusters such as the Institut Pasteur cluster.
• API and Library Support: Interfaces with Galaxy via the Galaxy API or the Bioblend library for remote invocation and data exchange.

Scientific Applications:

• Genomic Research: Enables selection and extraction of variants for population genetics, disease association studies, and evolutionary biology.
• Metagenomics and Phylogenetics: Supports metagenomic analyses and phylogenetic workflows, as exemplified by integration with MetaGenSense and NGphylogeny.fr.

Methodology:

Variant selection workflows are executed via the Galaxy platform and invoked through the Galaxy API or the Bioblend library, with execution on the Institut Pasteur high-performance computing cluster.