{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T13:33:47Z","timestamp":1793712827966,"version":"4.6.1"},"reference-count":36,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2014,11,25]],"date-time":"2014-11-25T00:00:00Z","timestamp":1416873600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/s12859-014-0356-4","type":"journal-article","created":{"date-parts":[[2014,11,24]],"date-time":"2014-11-24T15:04:33Z","timestamp":1416841473000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2964,"title":["ANGSD: Analysis of Next Generation Sequencing Data"],"prefix":"10.1186","volume":"15","author":[{"given":"Thorfinn Sand","family":"Korneliussen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anders","family":"Albrechtsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rasmus","family":"Nielsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2014,11,25]]},"reference":[{"issue":"6","key":"356_CR1","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1038\/nrg2986","volume":"12","author":"R Nielsen","year":"2011","unstructured":"Nielsen R, Paul JS, Albrechtsen A, Song YS: Genotype and SNP calling from next-generation sequencing data . Nat Rev Genet. 2011, 12 (6): 443-451. 10.1038\/nrg2986.","journal-title":"Nat Rev Genet"},{"key":"356_CR2","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform . Bioinformatics. 2009, 25: 1754-1760. 10.1093\/bioinformatics\/btp324.","journal-title":"Bioinformatics"},{"key":"356_CR3","doi-asserted-by":"publisher","first-page":"1966","DOI":"10.1093\/bioinformatics\/btp336","volume":"25","author":"R Li","year":"2009","unstructured":"Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J: SOAP2: an improved ultrafast tool for short read alignment . Bioinformatics. 2009, 25: 1966-1967. 10.1093\/bioinformatics\/btp336.","journal-title":"Bioinformatics"},{"issue":"3","key":"356_CR4","doi-asserted-by":"publisher","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","volume":"10","author":"B Langmead","year":"2009","unstructured":"Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome . Genome Biol. 2009, 10 (3): R25-10.1186\/gb-2009-10-3-r25.","journal-title":"Genome Biol"},{"issue":"12","key":"356_CR5","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1038\/nmeth.2221","volume":"9","author":"S Marco-Sola","year":"2012","unstructured":"Marco-Sola S, Sammeth M, Guigo R, Ribeca P: The GEM mapper: fast, accurate and versatile alignment by filtration . Nat Methods. 2012, 9 (12): 1185-1188. 10.1038\/nmeth.2221.","journal-title":"Nat Methods"},{"issue":"6","key":"356_CR6","doi-asserted-by":"publisher","first-page":"1124","DOI":"10.1101\/gr.088013.108","volume":"19","author":"R Li","year":"2009","unstructured":"Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J: SNP detection for massively parallel whole-genome resequencing . Genome Res. 2009, 19 (6): 1124-1132. 10.1101\/gr.088013.108.","journal-title":"Genome Res"},{"key":"356_CR7","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1186\/1471-2105-13-221","volume":"13","author":"CR Cabanski","year":"2012","unstructured":"Cabanski CR, Cavin K, Bizon C, Wilkerson MD, Parker JS, Wilhelmsen KC, Perou CM, Marron JS, Hayes DN: ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data . BMC Bioinformatics. 2012, 13: 221-10.1186\/1471-2105-13-221.","journal-title":"BMC Bioinformatics"},{"issue":"9","key":"356_CR8","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","volume":"20","author":"A McKenna","year":"2010","unstructured":"McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data . Genome Res. 2010, 20 (9): 1297-1303. 10.1101\/gr.107524.110.","journal-title":"Genome Res"},{"issue":"7","key":"356_CR9","doi-asserted-by":"publisher","first-page":"e37558","DOI":"10.1371\/journal.pone.0037558","volume":"7","author":"R Nielsen","year":"2012","unstructured":"Nielsen R, Korneliussen T, Albrechtsen A, Li Y, Wang J: SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data . PLoS ONE. 2012, 7 (7): e37558-10.1371\/journal.pone.0037558.","journal-title":"PLoS ONE"},{"key":"356_CR10","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1186\/1471-2105-12-231","volume":"12","author":"SY Kim","year":"2011","unstructured":"Kim SY, Lohmueller KE, Albrechtsen A, Li Y, Korneliussen T, Tian G, Grarup N, Jiang T, Andersen G, Witte D, Jorgensen T, Hansen T, Pedersen O, Wang J, Nielsen R: Estimation of allele frequency and association mapping using next-generation sequencing data . BMC Bioinformatics. 2011, 12: 231-10.1186\/1471-2105-12-231.","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"356_CR11","doi-asserted-by":"publisher","first-page":"430","DOI":"10.1002\/gepi.21636","volume":"36","author":"L Skotte","year":"2012","unstructured":"Skotte L, Korneliussen TS, Albrechtsen A: Association testing for next-generation sequencing data using score statistics . Genet Epidemiol. 2012, 36 (5): 430-437. 10.1002\/gepi.21636.","journal-title":"Genet Epidemiol"},{"key":"356_CR12","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1186\/1471-2105-14-289","volume":"14","author":"T Korneliussen","year":"2013","unstructured":"Korneliussen T, Moltke I, Albrechtsen A, Nielsen R: Calculation of Tajima\u2019s D and other neutrality test statistics from low depth next-generation sequencing data . BMC Bioinformatics. 2013, 14: 289-10.1186\/1471-2105-14-289. [http:\/\/www.biomedcentral.com\/1471-2105\/14\/289],","journal-title":"BMC Bioinformatics"},{"issue":"11","key":"356_CR13","doi-asserted-by":"publisher","first-page":"1852","DOI":"10.1101\/gr.157388.113","volume":"23","author":"FG Vieira","year":"2013","unstructured":"Vieira FG, Fumagalli M, Albrechtsen A, Nielsen R: Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation . Genome Res. 2013, 23 (11): 1852-1861. 10.1101\/gr.157388.113.","journal-title":"Genome Res"},{"issue":"3","key":"356_CR14","doi-asserted-by":"publisher","first-page":"979","DOI":"10.1534\/genetics.113.154740","volume":"195","author":"M Fumagalli","year":"2013","unstructured":"Fumagalli M, Vieira FG, Korneliussen TS, Linderoth T, Huerta-Sanchez E, Albrechtsen A, Nielsen R: Quantifying population genetic differentiation from next-generation sequencing data . Genetics. 2013, 195 (3): 979-992. 10.1534\/genetics.113.154740.","journal-title":"Genetics"},{"key":"356_CR15","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform . Bioinformatics. 2009, 25: 1754-1760. 10.1093\/bioinformatics\/btp324.","journal-title":"Bioinformatics"},{"issue":"6","key":"356_CR16","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1016\/j.ajhg.2009.11.004","volume":"85","author":"BL Browning","year":"2009","unstructured":"Browning BL, Yu Z: Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies . Am J Hum Genet. 2009, 85 (6): 847-861. 10.1016\/j.ajhg.2009.11.004.","journal-title":"Am J Hum Genet"},{"issue":"10","key":"356_CR17","doi-asserted-by":"publisher","first-page":"1486","DOI":"10.1093\/bioinformatics\/btu041","volume":"30","author":"M Fumagalli","year":"2014","unstructured":"Fumagalli M, Vieira FG, Linderoth T, Nielsen R: ngsTools: methods for population genetics analyses from next-generation sequencing data . Bioinformatics. 2014, 30 (10): 1486-1487. 10.1093\/bioinformatics\/btu041.","journal-title":"Bioinformatics"},{"issue":"3","key":"356_CR18","doi-asserted-by":"publisher","first-page":"1065","DOI":"10.1534\/genetics.112.145037","volume":"192","author":"N Patterson","year":"2012","unstructured":"Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D: Ancient admixture in human history . Genetics. 2012, 192 (3): 1065-1093. 10.1534\/genetics.112.145037.","journal-title":"Genetics"},{"issue":"7282","key":"356_CR19","doi-asserted-by":"publisher","first-page":"757","DOI":"10.1038\/nature08835","volume":"463","author":"M Rasmussen","year":"2010","unstructured":"Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MT, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, et al: Ancient human genome sequence of an extinct Palaeo-Eskimo . Nature. 2010, 463 (7282): 757-762. 10.1038\/nature08835.","journal-title":"Nature"},{"issue":"7456","key":"356_CR20","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1038\/nature12323","volume":"499","author":"L Orlando","year":"2013","unstructured":"Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, Malaspinas AS, Vogt J, Szklarczyk D, Kelstrup CD, Vinther J, Dolocan A, Stenderup J, Velazquez AM, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, et al: Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse . Nature. 2013, 499 (7456): 74-78. 10.1038\/nature12323.","journal-title":"Nature"},{"issue":"11","key":"356_CR21","doi-asserted-by":"publisher","first-page":"969","DOI":"10.1038\/ng.680","volume":"42","author":"Y Li","year":"2010","unstructured":"Li Y, Vinckenbosch N, Tian G, Huerta-Sanchez E, Jiang T, Jiang H, Albrechtsen A, Andersen G, Cao H, Korneliussen T, Grarup N, Guo Y, Hellman I, Jin X, Li Q, Liu J, Liu X, Spars\u00f8 T, Tang M, Wu H, Wu R, Yu C, Zheng H, Astrup A, Bolund L, Holmkvist J, J\u00f8rgensen T, Kristiansen K, Schmitz O, Schwartz TW, et al: Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants . Nat Genet. 2010, 42 (11): 969-972. 10.1038\/ng.680.","journal-title":"Nat Genet"},{"issue":"3","key":"356_CR22","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1534\/genetics.113.154138","volume":"195","author":"L Skotte","year":"2013","unstructured":"Skotte L, Korneliussen TS, Albrechtsen A: Estimating individual admixture proportions from next generation sequencing data . Genetics. 2013, 195 (3): 693-702. 10.1534\/genetics.113.154138.","journal-title":"Genetics"},{"issue":"21","key":"356_CR23","doi-asserted-by":"publisher","first-page":"2987","DOI":"10.1093\/bioinformatics\/btr509","volume":"27","author":"H Li","year":"2011","unstructured":"Li H: A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data . Bioinformatics. 2011, 27 (21): 2987-2993. 10.1093\/bioinformatics\/btr509.","journal-title":"Bioinformatics"},{"key":"356_CR24","doi-asserted-by":"publisher","first-page":"710","DOI":"10.1126\/science.1188021","volume":"328","author":"RE Green","year":"2010","unstructured":"Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prufer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Hober B, Hoffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, et al: A draft sequence of the Neandertal genome . Science. 2010, 328: 710-722. 10.1126\/science.1188021.","journal-title":"Science"},{"issue":"7319","key":"356_CR25","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.1038\/nature09534","volume":"467","author":"TGP Consortium","year":"2010","unstructured":"Consortium TGP: A map of human genome variation from population-scale sequencing . Nature. 2010, 467 (7319): 1061-1073. 10.1038\/nature09534. [http:\/\/www.nature.com\/nature\/journal\/v467\/n7319\/full\/nature09534.html],","journal-title":"Nature"},{"issue":"3","key":"356_CR26","doi-asserted-by":"publisher","first-page":"723","DOI":"10.1093\/molbev\/mst229","volume":"31","author":"E Han","year":"2014","unstructured":"Han E, Sinsheimer JS, Novembre J: Characterizing bias in population genetic inferences from low-coverage sequencing data . Mol Biol Evol. 2014, 31 (3): 723-735. 10.1093\/molbev\/mst229.","journal-title":"Mol Biol Evol"},{"issue":"11","key":"356_CR27","doi-asserted-by":"publisher","first-page":"2534","DOI":"10.1093\/molbev\/msq148","volume":"27","author":"A Albrechtsen","year":"2010","unstructured":"Albrechtsen A, Nielsen FC, Nielsen R: Ascertainment biases in SNP chips affect measures of population divergence . Mol Biol Evol. 2010, 27 (11): 2534-2547. 10.1093\/molbev\/msq148.","journal-title":"Mol Biol Evol"},{"issue":"29","key":"356_CR28","doi-asserted-by":"publisher","first-page":"11983","DOI":"10.1073\/pnas.1019276108","volume":"108","author":"S Gravel","year":"2011","unstructured":"Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA, Bustamante CD, Altshuler DL, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A, Clark AG, Collins FS, De la Vega FM, Donnelly P, Egholm M, Flicek P, Gabriel SB, Gibbs RA, Knoppers BM, Lander ES, Lehrach H, Mardis ER, McVean GA, Nickerson DA, Peltonen L, Schafer AJ, et al: Demographic history and rare allele sharing among human populations . Proc Natl Acad Sci U S A. 2011, 108 (29): 11983-11988. 10.1073\/pnas.1019276108.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"16","key":"356_CR29","doi-asserted-by":"publisher","first-page":"2064","DOI":"10.1093\/bioinformatics\/btq322","volume":"26","author":"G Ewing","year":"2010","unstructured":"Ewing G, Hermisson J: MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus . Bioinformatics. 2010, 26 (16): 2064-2065. 10.1093\/bioinformatics\/btq322.","journal-title":"Bioinformatics"},{"issue":"6104","key":"356_CR30","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1126\/science.1224344","volume":"338","author":"M Meyer","year":"2012","unstructured":"Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prufer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andres AM, Eichler EE, et al: A high-coverage genome sequence from an archaic Denisovan individual . Science. 2012, 338 (6104): 222-226. 10.1126\/science.1224344.","journal-title":"Science"},{"issue":"7481","key":"356_CR31","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1038\/nature12736","volume":"505","author":"M Raghavan","year":"2014","unstructured":"Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A, Moltke I, Rasmussen S, Stafford TW, Orlando L, Metspalu E, Karmin M, Tambets K, Rootsi S, Magi R, Campos PF, Balanovska E, Balanovsky O, Khusnutdinova E, Litvinov S, Osipova LP, Fedorova SA, Voevoda MI, DeGiorgio M, Sicheritz-Ponten T, Brunak S, Demeshchenko S, Kivisild T, Villems R, Nielsen R, Jakobsson M, et al: Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans . Nature. 2014, 505 (7481): 87-91. 10.1038\/nature12736.","journal-title":"Nature"},{"issue":"7327","key":"356_CR32","doi-asserted-by":"publisher","first-page":"1053","DOI":"10.1038\/nature09710","volume":"468","author":"D Reich","year":"2010","unstructured":"Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, Paabo S: Genetic history of an archaic hominin group from Denisova Cave in Siberia . Nature. 2010, 468 (7327): 1053-1060. 10.1038\/nature09710.","journal-title":"Nature"},{"issue":"5","key":"356_CR33","doi-asserted-by":"publisher","first-page":"833","DOI":"10.1101\/gr.146084.112","volume":"23","author":"Y Wang","year":"2013","unstructured":"Wang Y, Lu J, Yu J, Gibbs RA, Yu F: An integrative variant analysis pipeline for accurate genotype\/haplotype inference in population NGS data . Genome Res. 2013, 23 (5): 833-842. 10.1101\/gr.146084.112.","journal-title":"Genome Res"},{"key":"356_CR34","doi-asserted-by":"publisher","first-page":"274","DOI":"10.1186\/1471-2105-14-274","volume":"14","author":"X Yu","year":"2013","unstructured":"Yu X: Sun S: Comparing a few SNP calling algorithms using low-coverage sequencing data . BMC Bioinformatics. 2013, 14: 274-10.1186\/1471-2105-14-274.","journal-title":"BMC Bioinformatics"},{"issue":"8","key":"356_CR35","doi-asserted-by":"publisher","first-page":"1157","DOI":"10.1093\/bioinformatics\/btr076","volume":"27","author":"H Li","year":"2011","unstructured":"Li H: Improving SNP discovery by base alignment quality . Bioinformatics. 2011, 27 (8): 1157-1158. 10.1093\/bioinformatics\/btr076.","journal-title":"Bioinformatics"},{"issue":"7164","key":"356_CR36","doi-asserted-by":"publisher","first-page":"851","DOI":"10.1038\/nature06258","volume":"449","author":"KA Frazer","year":"2007","unstructured":"Frazer KA, Ballinger DGEa: A second generation human haplotype map of over 3.1 million SNPs . Nature. 2007, 449 (7164): 851-861. 10.1038\/nature06258.","journal-title":"Nature"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-014-0356-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0356-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0356-4","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0356-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,2,26]],"date-time":"2019-02-26T07:42:45Z","timestamp":1551166965000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-014-0356-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,11,25]]},"references-count":36,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["356"],"URL":"https:\/\/doi.org\/10.1186\/s12859-014-0356-4","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,11,25]]},"assertion":[{"value":"28 June 2014","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 October 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 November 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"356"}}