ANGSD protocols

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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

 (16)
2018
PMCID: 5783331
PMID: 29364919
DOI: 10.1371/journal.pone.0190555

[…] a statistical method based on genotype probabilities, rather than fixed called entities. this approach has been shown to be suitable for low or variable sequencing depth []. we used the software angsd v.0.911 [] to filter low quality data and calculate genotype posterior probabilities with an informative prior under the assumption of hardy weinberg equilibrium (hwe). we estimated […]

2018
PMCID: 5843647
PMID: 29520061
DOI: 10.1038/s41467-018-03384-9

[…] genotype likelihoods and the folded site frequency spectrum from the bam files. second, we used this site frequency spectrum as prior to calculate diversity measures (e.g. π, tajima’s d), using the angsd commands dothetas followed by thetastat make_bed and do_stat. this yielded diversity measures for 14,907 transcripts that were also expressed in the abdomen. differences in tajima’s d and π […]

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

[…] 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 (). covariance matrices were converted into pca outputs and visualized using r (). for the phylogenetic analyses, we performed […]

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

[…] et al. 2009). the autosomal heterozygosity was estimated from sample allele frequencies, taking genotype likelihoods into account for each species representative using angsdv0.913 (). 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 […]

2017
PMCID: 5427492
PMID: 28108551
DOI: 10.1534/g3.117.039008

[…] genotype calling by samtools are more biased than those by gatk. the correct-call rate among individuals by the proposed method (bgc) is higher than that by gatk, and lower than that by samtools and angsd when f is zero or minimized. when f is maximized, the correct-call rate by bgc is the highest. the highest correct-call rate among individuals by samtools and angsd when f is zero or minimized […]


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ANGSD in publications

 (85)
PMCID: 5941068
PMID: 29739910
DOI: 10.1128/mBio.00381-18

[…] between isolates using principal-component analysis (pca) implemented in snprelate v.1.10.2 (). summary statistics were computed using vcftools (). neutrality tests were performed using angsd (). genetic clustering was performed using ngsadmix () and faststructure ()., the linkage disequilibrium was calculated as r2, which indicates the square of the correlation coefficient […]

PMCID: 5924540
PMID: 29642393
DOI: 10.3390/genes9040198

[…] (“sort”) and collapse sequences with identical 5’ mapping coordinates (“rmdup”). finally, a consensus sequence was generated for each individual, based on maximum effective read depth [] using angsd v0.916 []. besides assembling the ngs short reads, we retrieved three assembled giant panda mitochondrial genomes from genbank [,,] which, together with the sequences from our two individuals, […]

PMCID: 5938232
PMID: 29740610
DOI: 10.1126/sciadv.aaq0392

[…] is found in the supplementary materials., we thank the staff of the danish national high-throughput dna sequencing center for the technical support, t. korneliussen for the technical help with angsd (analysis of next-generation sequencing data), and m. schubert for the access to y chromosome scaffolds for the horse. we thank the animal health trust and the donkey sanctuary for the support. […]

PMCID: 5879695
PMID: 29531040
DOI: 10.1073/pnas.1719880115

[…] ()., postmortem damage was assessed using mapdamage 2.0 (). contamination was estimated from the mitochondrial capture data using the approach of fu et al. () and for all male shotgun data using angsd () (si appendix, section 8 and table s34)., we performed demographic analysis of our ancient samples using two main approaches. in the first, we capitalized on our high coverage at the 5-mb […]

PMCID: 5844911
PMID: 29523798
DOI: 10.1038/s41598-018-22478-4

[…] organelle genome sequences using bowtie2 to generate a sam file. based on the sam file, samtools was used to create, sort and index bam files for snp calling. snp calls were conducted using the angsd pipeline with the parameter settings given in electronic supplementary material (esm), and they were based on allele frequencies that were estimated with genotype likelihoods […]


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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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