mpileup_vcf

mpileup_vcf converts sequencing coverage and single nucleotide polymorphism (SNP) information into Variant Call Format (VCF) files for variant calling and downstream genomic analyses.

Key Features:

• SNP and coverage analysis: Processes sequencing data to identify coverage depth and single nucleotide polymorphisms (SNPs) across genomic regions.
• VCF generation: Compiles identified variants and associated metrics into Variant Call Format (VCF) files.
• Galaxy@Pasteur integration: Operates within the Galaxy@Pasteur instance as an execution component for bioinformatics workflows.
• Galaxy API / Bioblend interface: Interfaces with Galaxy using the Galaxy API or the Bioblend library for workflow execution and job submission.
• Cluster execution: Executes computational tasks on the Institut Pasteur high-performance cluster infrastructure.

Scientific Applications:

• Genetic association studies: Provides VCF outputs used to identify genotype-phenotype associations.
• Evolutionary biology: Supplies variant data for analyses of genetic diversity and evolutionary relationships.
• Personalized medicine: Produces variant calls that can inform individual genetic assessments and clinical interpretation.
• Population genetics: Enables population-scale variant frequency and structure analyses using VCF-formatted data.
• Disease genomics: Facilitates detection of disease-associated variants and comparative analyses across samples.

Methodology:

Analyzes sequencing data to determine coverage depth and call SNPs, compiles variants into VCF files, and executes these steps within Galaxy workflows using the Galaxy API/Bioblend on the Institut Pasteur cluster.