reformat_snpeff_for_syntview

reformat_snpeff_for_syntview converts tabular snpEff outputs into SynTView-compatible .snp and .indel files for downstream visualization and analysis of single nucleotide polymorphisms and insertions/deletions.

Key Features:

• Conversion Capability: Parses tabular snpEff output and reformats variant annotations into .snp and .indel files compatible with SynTView.
• Integration with Galaxy@Pasteur: Implemented for use within the Galaxy@Pasteur instance to leverage Galaxy's computational framework for reproducibility and traceability.
• Execution via Galaxy API/Bioblend: Supports invocation through the Galaxy API or the Bioblend library to run on the Institut Pasteur compute cluster.

Scientific Applications:

• Genetic Variation Analysis: Enables visualization and analysis of SNPs and indels in SynTView using snpEff annotations.
• Metagenomic Data Integration: Integrates into Galaxy@Pasteur workflows that interface with services such as MetaGenSense for metagenomic variant analyses.

Methodology:

Processes tabular snpEff files to generate .snp and .indel outputs and executes within the Galaxy@Pasteur environment via the Galaxy API or the Bioblend library on the Institut Pasteur cluster.