ANGSD

ANGSD analyzes next-generation sequencing (NGS) data to compute and use genotype likelihoods for estimating population genetic summary statistics and performing association analyses while accounting for genotype uncertainty.

Key Features:

• Versatile Input Handling: Supports mapped reads (BAM), raw sequencing reads, and imputed genotype probability files (BEAGLE), and can operate on genotype likelihoods.
• Genotype Uncertainty Management: Incorporates genotype likelihoods to account for uncertainty in low- and medium-depth sequencing data.
• Comprehensive Analytical Capabilities: Computes a wide array of summary statistics and performs population genetic analyses and association mapping using information from reads or genotype likelihoods.
• Methodological Flexibility: Supports combinations of existing statistical methods to implement diverse analytical approaches.
• High Performance and Efficiency: Implements multithreading and is optimized for efficient memory usage and fast processing of large sample sets.
• Implementation: Implemented in C/C++.

Scientific Applications:

• Population Genetics: Infer evolutionary processes, population structure, and demographic history from NGS data.
• Association Mapping: Identify genetic variants associated with traits or diseases using likelihood-based analyses.
• Genomic Diversity Studies: Estimate genomic diversity and signals of adaptation across species while accounting for genotype uncertainty.

Methodology:

Operates on genotype likelihoods derived from mapped reads or on precomputed genotype probabilities (e.g., BEAGLE), computes summary statistics, and performs population genetic analyses and association mapping in a multithreaded C/C++ implementation.