Citing angsd - Revision history

Thorfinn: /* Contamination */

2015-08-31T08:08:34Z

Contamination

← Older revision		Revision as of 10:08, 31 August 2015
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	===Contamination ===		===Contamination ===
	from X chromosome [[Rasmussen2011]]		from X chromosome [[Rasmussen2011]]
			===Relatedness===
			http://bioinformatics.oxfordjournals.org/content/early/2015/08/29/bioinformatics.btv509.full.pdf?keytype=ref&ijkey=ZQbzsWISGPWpPOg

2014-11-26T08:51:51Z

← Older revision		Revision as of 10:51, 26 November 2014
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	year = {2014},		year = {2014},
	pages = {356},		pages = {356},
	~~file = {Full Text PDF:files/10/Korneliussen et al. - 2014 - ANGSD Analysis of Next Generation Sequencing Data.pdf:application/pdf;Snapshot:files/19/abstract.html:text/html}~~
	}		}
	</pre>		</pre>

2014-11-26T08:51:17Z

← Older revision		Revision as of 10:51, 26 November 2014
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	~~Currently there~~ is ~~not publication for~~ angsd. ~~However~~, ~~many~~ of ~~the methods implemented here~~ are ~~published~~.		There is an overall angsd paper with bibtex below.
			<pre>
			@article{korneliussen_angsd:_2014,
			title = {{ANGSD}: Analysis of Next Generation Sequencing Data},
			volume = {15},
			copyright = {http://creativecommons.org/licenses/by/2.0/},
			issn = {1471-2105},
			shorttitle = {{ANGSD}},
			url = {http://www.biomedcentral.com/1471-2105/15/356/abstract},
			doi = {10.1186/s12859-014-0356-4},
			abstract = {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.},
			language = {en},
			number = {1},
			urldate = {2014-11-26},
			journal = {{BMC} Bioinformatics},
			author = {Korneliussen, Thorfinn S. and Albrechtsen, Anders and Nielsen, Rasmus},
			month = nov,
			year = {2014},
			pages = {356},
			file = {Full Text PDF:files/10/Korneliussen et al. - 2014 - ANGSD Analysis of Next Generation Sequencing Data.pdf:application/pdf;Snapshot:files/19/abstract.html:text/html}
			}
			</pre>


	==Methods==		==Methods==

2014-06-27T12:34:17Z

← Older revision		Revision as of 14:34, 27 June 2014
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	===Error rates method 2===		===Error rates method 2===
	based on a high quality genome [[orlando2013]]		based on a high quality genome [[orlando2013]]


			===Contamination ===
			from X chromosome [[Rasmussen2011]]

2014-01-16T00:52:47Z

SNP calling

← Older revision		Revision as of 02:52, 16 January 2014
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	===SNP calling===		===SNP calling===
	SNP calling based on genotype likelihoods		SNP calling based on genotype likelihoods
	; -~~doSNP~~		; -SNP_pval
	[[kim2011]]		[[kim2011]]

2014-01-03T12:16:15Z

Methods

← Older revision		Revision as of 14:16, 3 January 2014
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	===Admixture===		===Admixture===
	http://www.popgen.dk/software/index.php/NgsAdmix#Citation		http://www.popgen.dk/software/index.php/NgsAdmix#Citation

			===Error rates method 1===
			joint GL and error estimation [[kim2011]]
			===Error rates method 2===
			based on a high quality genome [[orlando2013]]

2013-11-25T18:06:07Z

Admixture

← Older revision		Revision as of 20:06, 25 November 2013
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	===Admixture===		===Admixture===
			http://www.popgen.dk/software/index.php/NgsAdmix#Citation

2013-11-25T18:05:17Z

Neutrality tests (eg Tajima)

2013-10-02T17:28:42Z

SFS estimation

← Older revision		Revision as of 19:28, 2 October 2013
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	===SFS estimation===		===SFS estimation===
	Estimating the site frequency spectrum [[Nielsen2012]]		Estimating the site frequency spectrum [[Nielsen2012]]

			===Neutrality tests (eg Tajima)===
			[[Korneliussen2013]]

2013-06-29T09:40:18Z

← Older revision		Revision as of 11:40, 29 June 2013
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	Currently there is not publication for angsd. However, many of the ~~method~~ implemented here are published.		Currently there is not publication for angsd. However, many of the methods implemented here are published.

	==Methods==		==Methods==