ArrayMaker

ArrayMaker extracts SNP genotypes from whole-genome alignments to provide standardized genotype data for downstream genetic analyses.

Key Features:

• Accurate Genotype Extraction: Efficiently extracts SNP genotypes at pre-defined loci from whole-genome alignments and genotyping-by-sequencing data.
• Standardized Output Format: Outputs genotypes in formats compatible with association analysis software and datasets from commercial array platforms.
• Data Sharing and Compatibility: Standardized outputs facilitate integration and comparison of genotyping data across multiple technologies for collaborative research and meta-analyses.

Scientific Applications:

• Genome-Wide Association Studies (GWAS): Provides accurate genotype data required for identifying associations between genetic variants and traits.
• Fine Mapping: Assists in refining regions of interest to pinpoint causal variants identified in GWAS.
• Candidate Variant Assessment: Enables detailed analysis of specific genetic variants implicated in disease or phenotypic variation.
• Data Integration and Sharing: Supports the integration of genotyping data from diverse sources to enable collaborative studies and meta-analyses.

Methodology:

ArrayMaker is implemented in Perl and runs on Linux; it processes whole-genome alignments to extract SNP genotypes at user-defined loci and produces outputs compatible with standard genotyping formats and association analysis software.