ANGSD specifications

Information


Unique identifier OMICS_16021
Name ANGSD
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM, VCF, CRAM
Output format TXT
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements ZLIB
Maintained Yes

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Maintainer


  • person_outline Thorfinn Sand Korneliussen <>

ANGSD article

ANGSD citations

 (3)
2018
PMCID: 5913678

[…] to single nucleotide polymorphisms (snps) occurring in at least two individuals. this was done to remove singletons, which could represent sequencing errors. we computed genotype likelihoods in angsd and converted outputs to a covariance matrix using ngstools (fumagalli et al. 2014). covariance matrices were converted into pca outputs and visualized using r (r development core team 2008). […]

2017
PMCID: 5683586

[…] (https://github.com/johnomics/martin_davey_jiggins_evaluating_introgression_statistics), which makes use of the egglib library [88]. the input file was generated by first identifying genotypes using angsd (-domajorminor 1 -domaf 1 -gl 2 -dogeno 4 -dopost 1 -postcutoff 0.95 -snp_pval 1e−6) followed by format adjustments with a custom script (see “availability of data and materials”). outliers […]

2017
PMCID: 5737861

[…] correlation values of exon expression the same way as for gene expression (described earlier)., gene isoforms in the six species of cichlids were extracted from the assembled transcriptomes using angsd (korneliussen etal. 2014) and bedtools (quinlan and hall 2010). transdecoder (http://transdecoder.github.io) was used to de novo annotate open reading frames orfs in the expressed transcripts […]

ANGSD institution(s)
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark; Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Department of Integrative Biology and Statistics, UC-Berkeley, Berkeley, CA, USA
ANGSD funding source(s)
Supported by Danish National Research Foundation (DNRF94), the Villum Foundation, and grant 2R14003229-07 from the National Institutes of Health.

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