ANGSD: analysis of next generation sequencing data

TY - JOUR

T1 - ANGSD

T2 - analysis of next generation sequencing data

AU - Korneliussen, Thorfinn Sand

AU - Albrechtsen, Anders

AU - Nielsen, Rasmus

PY - 2014/11/25

Y1 - 2014/11/25

N2 - Background: High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are needed in order to facilitate analyses of thousands of samples simultaneously. Results: We present a multithreaded program suite called ANGSD. This program can calculate various summary statistics, and perform association mapping and population genetic analyses utilizing the full information in next generation sequencing data by working directly on the raw sequencing data or by using genotype likelihoods. Conclusions: The open source c/c++ program ANGSD is available at . The program is tested and validated on GNU/Linux systems. The program facilitates multiple input formats including BAM and imputed beagle genotype probability files. The program allow the user to choose between combinations of existing methods and can perform analysis that is not implemented elsewhere.

AB - Background: High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are needed in order to facilitate analyses of thousands of samples simultaneously. Results: We present a multithreaded program suite called ANGSD. This program can calculate various summary statistics, and perform association mapping and population genetic analyses utilizing the full information in next generation sequencing data by working directly on the raw sequencing data or by using genotype likelihoods. Conclusions: The open source c/c++ program ANGSD is available at . The program is tested and validated on GNU/Linux systems. The program facilitates multiple input formats including BAM and imputed beagle genotype probability files. The program allow the user to choose between combinations of existing methods and can perform analysis that is not implemented elsewhere.

U2 - 10.1186/s12859-014-0356-4

DO - 10.1186/s12859-014-0356-4

M3 - Journal article

C2 - 25420514

SN - 1471-2105

VL - 15

JO - B M C Bioinformatics

JF - B M C Bioinformatics

M1 - 356

ER -