glactools

glactools provides command-line utilities to manage, manipulate, and analyze per-individual genotype likelihoods and population-level allele counts for population genomics research.

Key Features:

• Data import and intermediate representation: Import genotypic data or population-wide allele counts into a flexible intermediate representation with two forms that store per-individual genotype likelihoods and aggregated allele counts across individuals.
• Data operations and manipulation: Perform dataset intersections, merge individual samples into populations, and create subsets of genomic data.
• Querying capabilities: Identify genetic sites where specific populations do not share alleles with other populations.
• Export capabilities: Export data to multiple file formats compatible with a range of population genetics software.
• Summary statistics computation: Compute summary statistics relevant to population genomics analyses.

Scientific Applications:

• Population genomics data management: Standardize and store genotype likelihoods and allele-count data for population-level analyses.
• Comparative population genetics: Detect population-specific alleles and compare genetic variation across populations.
• Preparation for downstream analyses: Generate exports in formats required by other population genetics tools and workflows.
• Reproducible analyses: Provide standardized intermediate representations to reduce ad hoc scripting and improve reproducibility of population-genomic workflows.

Methodology:

Implemented as C++ command-line utilities that link against the htslib library and operate on intermediate representations of genotype likelihoods and allele counts.