angsd-wrapper

angsd-wrapper implements a computational wrapper to the ANGSD software package to perform population-genetic analyses directly from next-generation sequencing (NGS) genotype likelihoods, enabling analysis without prior SNP calling.

Key Features:

• Probabilistic genotype-likelihood analysis: Uses genotype likelihoods to perform population genetic inference without requiring discrete SNP calls.
• SNP-calling bypass and low-depth support: Bypasses traditional SNP calling and maximizes use of low-depth NGS data to improve accuracy of downstream analyses.
• Analytical repertoire: Supports nucleotide diversity estimation, neutrality tests, principal component analysis (PCA), admixture proportion estimation for individuals, and statistics quantifying recent introgression.
• ANGSD integration: Interfaces with the ANGSD software package to access its probabilistic population-genetic methods.

Scientific Applications:

• Population Genetics: Enables estimation of genetic diversity, population structure, and evolutionary parameters from NGS data using genotype likelihoods.
• Molecular Ecology: Supports studies of species interactions, adaptation, and conservation biology using NGS datasets, including low-depth sequencing.
• Comparative Genomics: Facilitates comparative analyses across populations or species, including analyses of wild and domesticated Zea (corn) populations.

Methodology:

Integrates with ANGSD and employs probabilistic models that directly utilize genotype likelihoods, thereby bypassing SNP calling and optimizing inference from NGS data.