Citing angsd

Currently there is not publication for angsd. However, many of the methods implemented here are published.

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