ngsRelateV2

ngsRelateV2 estimates pairwise relatedness from high-throughput sequencing (HTS) data, including inbred samples and low-coverage datasets where genotype calls are unreliable.

Key Features:

• Inbreeding consideration: Estimates relatedness among potentially inbred individuals by computing the 9 condensed Jacquard coefficients.
• Relatedness statistics: Reports a range of relatedness statistics and other relatedness metrics derived from sequence data.
• Low-coverage data handling: Enables relatedness estimation from low-coverage HTS data where reliable genotype calls are challenging.
• Performance optimization: Implements multi-threading that scales linearly with the number of processing cores for efficient computation.
• Data format compatibility: Accepts BAM/CRAM for raw sequence data and VCF/BCF for summary data.

Scientific Applications:

• Population and evolutionary genetics: Provides pairwise relatedness estimates for analyses in population genetics and evolutionary biology.
• Conservation and breeding studies: Supports relatedness and inbreeding analyses in conservation genetics and selective breeding contexts.
• Low-coverage sequencing projects: Enables kinship inference in studies constrained to low sequencing depth.

Methodology:

Derives the 9 condensed Jacquard coefficients and other relatedness metrics from HTS data using statistical methods, with calculations implemented using multi-threading.