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: Difference between revisions
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===Error rates method 2=== | ===Error rates method 2=== | ||
based on a high quality genome [[orlando2013]] | based on a high quality genome [[orlando2013]] | ||
===Contamination === | |||
from X chromosome [[Rasmussen2011]] | |||
Revision as of 13:34, 27 June 2014
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