LINKDATAGEN

LINKDATAGEN generates linkage mapping input files to enable genetic linkage analysis and the preparation of inputs for five linkage mapping software applications.

Key Features:

• Perl implementation: Implemented in Perl for processing and formatting genotype data.
• Multi-software output: Produces input files compatible with five different linkage mapping software applications.
• Versatile data compatibility: Processes genotype data from Affymetrix and Illumina SNP chips and SNP genotypes inferred from sequencing.
• Support for HAPMAP populations: Handles data from all 11 HAPMAP Phase III populations.
• Error checking: Incorporates rudimentary error checks and data validation to help ensure integrity of generated input files.
• Customizability: Allows amendment of its code and output formatting to accommodate specific linkage mapping preferences.

Scientific Applications:

• Genetic linkage analysis: Prepares input files required for mapping genetic loci associated with traits and diseases.
• Population genetics: Enables analyses that use genotype data from HAPMAP Phase III populations.
• Genome-wide association studies (GWAS): Facilitates preparation of genotype inputs used in GWAS and related analyses.

Methodology:

Parses genotype calls or SNP genotypes inferred from sequencing and formats them into compatible input files for linkage mapping programs, including data validation and rudimentary error checking.