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

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Currently there is not publication for angsd. However, many of the method 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

-doSNP

kim2011

Genotype likelihoods

-GL 1

same as in samtools Li2010

-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