ANGSD: Analysis of next generation Sequencing Data

Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.

Citing angsd

From angsd
Jump to navigation Jump to search

There is an overall angsd paper with bibtex below.

	title = {{ANGSD}: Analysis of Next Generation Sequencing Data},
	volume = {15},
	copyright = {},
	issn = {1471-2105},
	shorttitle = {{ANGSD}},
	url = {},
	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},


Maf estimation from counts of alleles



Allele estimation

allele estimation from genotype likelihoods

- doMaf


SNP calling

SNP calling based on genotype likelihoods



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


-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)



Error rates method 1

joint GL and error estimation kim2011

Error rates method 2

based on a high quality genome orlando2013


from X chromosome Rasmussen2011