ANGSD is a multithreaded program suite for analyzing next-generation sequencing (NGS) data. It calculates various summary statistics and performs association mapping and population genetic analyses by working directly on raw sequencing data or using genotype likelihoods (GLs). The program is open-source and available at http://www.popgen.dk/angsd. It supports multiple input formats, including BAM and imputed Beagle genotype probability files. ANGSD allows users to choose between existing methods and perform analyses not implemented elsewhere. ANGSD processes NGS data by aligning reads to a reference genome, calculating GLs based on mapping and sequencing quality scores, and then using these GLs for downstream analyses. It supports four GL models, including recalibrated SOAPsnp, original GATK, modified SAMtools, and type-specific error models. The program can estimate allele frequencies, perform population genetic analyses, and detect admixture using GLs. ANGSD is used for SNP discovery, genotype calling, and association studies. It allows for the use of GLs to account for uncertainty in genotypes, which is particularly important for low-coverage data. The program also supports the estimation of the joint site frequency spectrum (2D-SFS) and the ABBA-BABA D-statistic for detecting ancient admixture. ANGSD is compared to other tools like GATK and SAMtools in terms of computational speed and accuracy. It is faster in most scenarios and provides more accurate results, especially for low-coverage data. ANGSD supports various analyses, including population structure, inbreeding coefficients, and Fst statistics. It is also used for estimating allele frequencies and performing association tests. The program is available on Linux systems and supports C/C++ programming. It requires zlib and R for some analyses. ANGSD is freely available and has no restrictions for non-academic users. It is a versatile tool for NGS data analysis, offering a wide range of functionalities for population genetics and association studies.ANGSD is a multithreaded program suite for analyzing next-generation sequencing (NGS) data. It calculates various summary statistics and performs association mapping and population genetic analyses by working directly on raw sequencing data or using genotype likelihoods (GLs). The program is open-source and available at http://www.popgen.dk/angsd. It supports multiple input formats, including BAM and imputed Beagle genotype probability files. ANGSD allows users to choose between existing methods and perform analyses not implemented elsewhere. ANGSD processes NGS data by aligning reads to a reference genome, calculating GLs based on mapping and sequencing quality scores, and then using these GLs for downstream analyses. It supports four GL models, including recalibrated SOAPsnp, original GATK, modified SAMtools, and type-specific error models. The program can estimate allele frequencies, perform population genetic analyses, and detect admixture using GLs. ANGSD is used for SNP discovery, genotype calling, and association studies. It allows for the use of GLs to account for uncertainty in genotypes, which is particularly important for low-coverage data. The program also supports the estimation of the joint site frequency spectrum (2D-SFS) and the ABBA-BABA D-statistic for detecting ancient admixture. ANGSD is compared to other tools like GATK and SAMtools in terms of computational speed and accuracy. It is faster in most scenarios and provides more accurate results, especially for low-coverage data. ANGSD supports various analyses, including population structure, inbreeding coefficients, and Fst statistics. It is also used for estimating allele frequencies and performing association tests. The program is available on Linux systems and supports C/C++ programming. It requires zlib and R for some analyses. ANGSD is freely available and has no restrictions for non-academic users. It is a versatile tool for NGS data analysis, offering a wide range of functionalities for population genetics and association studies.