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
Currently there is not publication for angsd. However, many of the methods implemented here are published.
Methods
Maf estimation from counts of alleles
- -cutoff
Allele estimation
allele estimation from genotype likelihoods
- - doMaf
SNP calling
SNP calling based on genotype likelihoods
- -SNP_pval
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)
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