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 method 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
- -doSNP
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