Citing angsd: Difference between revisions

Latest revision as of 09:08, 31 August 2015

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

@@ Line 1: / Line 1: @@
-Currently there is not publication for angsd. However, many of the method implimented 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},
+}
+</pre>
 ==Methods==
+===Maf estimation from counts of alleles===
+; -cutoff
+[[Li2010]]
 ===Allele estimation===
@@ Line 10: / Line 35: @@
 ===SNP calling===
 SNP calling based on genotype likelihoods
-; -doSNP
+; -SNP_pval
 [[kim2011]]
 ===Genotype likelihoods===
 ; -GL 1
-same as in samtools [[Li2010]]
+same as in samtools [[Li2011]]
 ; -GL 2
 same as in [[gatk]]
@@ Line 29: / Line 54: @@
 ; -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