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ANGSD: Analysis of Next Generation Sequencing Data

ANGSD is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data. The software is written in C++ and has been used on large sample sizes.

This program is not for manipulating BAM/CRAM files, but solely a tool to perform various kinds of analysis. We recommend the excellent program SAMtools for outputting and modifying bamfiles.

ANGSD is also on github: https://github.com/ANGSD/angsd

Overview

ANGSD reads mapped reads or precomputed genotype likelihoods/probabilities, and most analyses work directly on the genotype likelihoods rather than on called genotypes.

flowchart LR
    i1["BAM / CRAM<br/>mpileup"] --> s1["Sequence data"]
    i2["VCF / BCF<br/>GLF / beagle"] --> s2["Genotype likelihoods"]
    i3["beagle"] --> s3["Genotype probabilities"]
    s1 --> s2 --> s3
    s1 --> a1["Depth and allele counts<br/>Error estimates<br/>Consensus / random-base fasta<br/>ABBABABA (D-stat)"]
    s2 --> a2["Allele frequencies and SNP calling<br/>SAF, SFS and thetas / neutrality tests<br/>Fst and PBS<br/>Admixture, inbreeding and HWE<br/>Association<br/>Genotype calling"]
    s3 --> a3["Genotype calling<br/>Allele frequencies<br/>Association<br/>SFS"]
    style i1 fill:#ffe0b2,stroke:#e65100
    style i2 fill:#ffe0b2,stroke:#e65100
    style i3 fill:#ffe0b2,stroke:#e65100
    style a1 fill:#bbdefb,stroke:#0d47a1
    style a2 fill:#bbdefb,stroke:#0d47a1
    style a3 fill:#bbdefb,stroke:#0d47a1

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See Input data for the supported formats and Filters for read and site filtering.

Synopsis

./angsd [OPTIONS]

example of allele frequency estimated from genotype likelihoods with bam files as input using 10 threads

./angsd -out outFileName -bam bam.filelist -GL 1 -doMaf 1 -doMajorMinor 1 -nThreads 10

Platform

The program is developed on tested on a Linux system with gcc compiler. It compiles on OSX with clang, but OSX is not really that tested.