ANGSD: Analysis of next generation Sequencing Data

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Citing angsd

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There is an overall angsd paper with bibtex below.

@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},
}


Methods

Maf estimation from counts of alleles

-cutoff

Li2010

Allele estimation

allele estimation from genotype likelihoods

- doMaf

kim2011

SNP calling

SNP calling based on genotype likelihoods

-SNP_pval

kim2011

Genotype likelihoods

-GL 1

same as in samtools Li2011

-GL 2

same as in gatk

-GL 3

same as in soapSNP

-GL 4

same as in kim2011

Association

-doAsso 2

using score statistic Skotte2012

-doAsso 1 or 3

using allele frequencies kim2011

SFS estimation

Estimating the site frequency spectrum Nielsen2012

Neutrality tests (eg Tajima)

Korneliussen2013

Admixture

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


Contamination

from X chromosome Rasmussen2011

Relatedness

http://bioinformatics.oxfordjournals.org/content/early/2015/08/29/bioinformatics.btv509.full.pdf?keytype=ref&ijkey=ZQbzsWISGPWpPOg