pileup_to_vcf

pileup_to_vcf converts pileup files into Variant Call Format (VCF) and applies integrated filtering to produce high-confidence variant calls for downstream genomic analyses.

Key Features:

• Conversion Capability: Converts pileup files that summarize base calls at each reference position into VCF files that record sequence variants.
• Integrated Filtering: Applies filtering criteria during conversion to retain high-confidence variant records and exclude low-confidence calls.
• Galaxy Integration: Executes within the Galaxy platform and can run on the Institut Pasteur cluster as the execution environment.

Scientific Applications:

• Genomic Variant Analysis: Produces VCF-formatted variant calls from sequencing pileup data for studies in genetics, evolutionary biology, and personalized medicine.
• Metagenomics Studies: Converts and filters sequencing-derived pileup data into VCF to support variant-level analyses in metagenomic datasets.

Methodology:

Operates within the Galaxy platform, utilizing the Galaxy API or the Bioblend library to communicate with the Institut Pasteur cluster.