ANGSD pipeline

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 <>

Publication for ANGSD

ANGSD IN pipelines

 (10)
2018
PMCID: 5913678
PMID: 29528428
DOI: 10.1093/molbev/msy037

[…] heterozygosity was estimated from sample allele frequencies, taking genotype likelihoods into account for each species representative using angsdv0.913 (korneliussen et al. 2014). the software angsd was chosen as it can overcome the biases that may arise due to differential coverage across the genome. instead of other methods that rely on direct snp/genotype calling from the data, angsd […]

2018
PMCID: 5913678
PMID: 29528428
DOI: 10.1093/molbev/msy037

[…] angsd was chosen as it can overcome the biases that may arise due to differential coverage across the genome. instead of other methods that rely on direct snp/genotype calling from the data, angsd uses genotype likelihoods in downstream analyses. this allows for the incorporation of statistical uncertainties into the analysis, which in turn reduce the biases caused by differential […]

2017
PMCID: 5683586
PMID: 29132403
DOI: 10.1186/s13059-017-1346-4

[…] (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 […]

2016
PMCID: 4915356
PMID: 26983554
DOI: 10.1093/molbev/msw051

[…] two complementary approaches for snp and genotype calling (supplementary fig. s1, supplementary material online): (1) direct estimation without calling genotypes was implemented in the software angsd v0.602 (korneliussen et al. 2014). only reads with a minimal mapping quality of 30 and bases with a minimal quality score of 20 were considered. for all filtered sites in both species, […]

2016
PMCID: 4915356
PMID: 26983554
DOI: 10.1093/molbev/msw051

[…] statistics that relied on inferred site-frequency-spectrum (sfs), estimation was performed directly from genotype likelihoods without calling genotypes (nielsen et al. 2011) as implemented in angsd (korneliussen et al. 2014). (2) for those estimations that required accurate genotype calls, single nucleotide polymorphisms (snps) and genotypes were called with haplotypecaller in gatk […]

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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