ANGSD: Analysis of next generation Sequencing Data

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Korneliussen2013

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Thorfinn Sand Korneliussen, Ida Moltke, Anders Albrechtsen and Rasmus Nielsen; Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data;

A description of how to use the method is described here: Tajima

Open Access

http://www.biomedcentral.com/1471-2105/14/289

Bibtex

@article{korneliussen_calculation_2013,
	title = {Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data},
	volume = {14},
	issn = {1471-2105},
	url = {http://www.biomedcentral.com/1471-2105/14/289},
	doi = {10.1186/1471-2105-14-289},
	abstract = {{BACKGROUND:A} number of different statistics are used for detecting natural selection using {DNA} sequencing data, including statistics that are summaries of the frequency spectrum, such as Tajima's D. These statistics are now often being applied in the analysis of Next Generation Sequencing ({NGS)} data. However, estimates of frequency spectra from {NGS} data are strongly affected by low sequencing coverage; the inherent technology dependent variation in sequencing depth causes systematic differences in the value of the statistic among genomic {regions.RESULTS:We} have developed an approach that accommodates the uncertainty of the data when calculating site frequency based neutrality test statistics. A salient feature of this approach is that it implicitly solves the problems of varying sequencing depth, missing data and avoids the need to infer variable sites for the analysis and thereby avoids ascertainment problems introduced by a {SNP} discovery {process.CONCLUSION:Using} an empirical Bayes approach for fast computations, we show that this method produces results for low-coverage {NGS} data comparable to those achieved when the genotypes are known without uncertainty. We also validate the method in an analysis of data from the 1000 genomes project. The method is implemented in a fast framework which enables researchers to perform these neutrality tests on a genome-wide scale.},
	number = {1},
	journal = {{BMC} Bioinformatics},
	author = {Korneliussen, Thorfinn and Moltke, Ida and Albrechtsen, Anders and Nielsen, Rasmus},
	year = {2013},
	pages = {289}
}

doi

doi:10.1186/1471-2105-14-289