ANGSD: Analysis of Next Generation Sequencing Data
Open accessAbstract
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 http://www.popgen.dk/angsd . 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.
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We excluded libraries with X-contamination estimates greater than 1.5%.
“we excluded libraries with X-contamination estimates greater than 1.5%32.”
From Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation (2018) · cites this paper as [32]
The study evaluated each individual for evidence of authentic ancient DNA by limiting to libraries with a minimum of 3% cytosine-to-thymine errors at the final nucleotide, requiring X-to-Y-chromosome ratio characteristic of sex, >95% matching to mtDNA consensus, and <2% contamination for males.
“We evaluated each individual for evidence of authentic ancient DNA by limiting to libraries with a minimum of 3% cytosine-to-thymine errors at the final nucleotide29, by requiring that the ratio of X-to-Y-chromosome sequences was characteristic of either a male or a female, by requiring >95% matching to the consensus sequence of mitochondrial DNA30, and by requiring (for males) a lack of variation”
From Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation (2018) · cites this paper as [32]
The citation is attached to the minimum 3% terminal cytosine-to-thymine error criterion. The ABBA-BABA section says transitions have high error rates in ancient genomes, but our copy does not give a 3% threshold or describe terminal-base errors as an authenticity test. Searches for those criteria found no supporting passage. (LLM, conf=0.74)
Experimental — accuracy not yet measuredWe assessed the quality of each library at the screening stage using three standard methods for determining ancient DNA authenticity: mitochondrial genome matching rate, C-to-T substitution rate, and X-chromosome contamination.
“We assessed the quality of each library at the screening stage using three standard methods for determining ancient DNA authenticity.”
From Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation (2018) · cites this paper as [32]
The Results and discussion > ABBA-BABA section (page unavailable) describes filtering error-prone transitions when analyzing an ancient Denisovan genome, not screening libraries for authenticity. Searches for mitochondrial matching rates, C-to-T substitution rates, and X-chromosome contamination found no passage describing the three claimed methods. (LLM, conf=0.77)
Experimental — accuracy not yet measuredNuclear contamination in males was estimated using ANGSD, which compares mismatch rates between polymorphic sites on the X chromosome.
“We next used ANGSD (v0.910) (41), which compares mismatch rates between polymorphic sites on the X chromosome to estimate nuclear contamination in males.”
From Ancient DNA sheds light on the genetic origins of early Iron Age Philistines (2019) · cites this paper as [41]
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- Authors
- Korneliussen, T. S., Albrechtsen, A., & Nielsen, R.
- Affiliations
- Natural History Museum of Denmark (DK)
- University of Copenhagen (DK)
- Corresponding author
- Korneliussen, Thorfinn Sand
- Venue
- BMC Bioinformatics
- Published
- 2014-11-25
- Volume
- 15
- Issue
- 1
- Pages
- 356-356
- ISSN
- 1471-2105 (ISSN-L)
- PMC
- PMC4248462
- OpenAlex
- W2129034036
- Cited by
- 2,982
- References
- 36
- Citations by year
- 2026: 332 · 2025: 419 · 2024: 401 · 2023: 335 · 2022: 356 · 2021: 364 · 2020: 233 · 2019: 188 · 2018: 143 · 2017: 97 · 2016: 74 · 2015: 28 · 2014: 2
- FWCI
- 27.45
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- BMC Bioinformatics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- Villum Fonden (00007171)
- National Research Foundation
- Danmarks Grundforskningsfond (DNRF94)
- National Institutes of Health (2R14003229, 2R14003229-07)
- U.S. Public Health Service (2R14003229-07)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- next-generation sequencing data analysis, association mapping, population genetics, genotype likelihoods, multithreaded programs, summary statistics, BAM files, imputed genotypes
- MeSH terms
- Gene Frequency, Genetics, Population, Genotype, Software, Likelihood Functions, Polymorphism, Single Nucleotide, High-Throughput Nucleotide Sequencing
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