AffyPipe

AffyPipe automates processing of genotyping data generated by Affymetrix Axiom arrays to produce PLINK-format genotype files for downstream genetic analyses.

Key Features:

• Workflow automation: Automates standard and best-practice workflows for any species genotyped on the Axiom platform by integrating Affymetrix Power Tools and the R package SNPolisher.
• Tool integration: Integrates three stand-alone Affymetrix Power Tools executables and the R package SNPolisher to reproduce steps previously run manually.
• PLINK export: Exports genotype calls directly in PLINK format for compatibility with downstream analysis software.
• SNP probe editing: Allows direct editing of SNP probe classes during processing to adjust probe classifications.

Scientific Applications:

• Genome-wide association studies (GWAS): Provides QCed, PLINK-format genotype data from Axiom arrays for association testing.
• Population genetics: Enables processing of Axiom genotyping datasets for population-level analyses.
• Evolutionary biology: Supports large-scale genotyping data preparation for evolutionary and comparative studies.

Methodology:

Integrates Affymetrix Power Tools executables and the R package SNPolisher into a cohesive pipeline that automates handling of raw Axiom genotyping output through quality control, normalization, annotation, and export to final PLINK-format genotype files.