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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===SFS estimation=== | ===SFS estimation=== | ||
Estimating the site frequency spectrum [[Nielsen2012]] | Estimating the site frequency spectrum [[Nielsen2012]] | ||
===Neutrality tests (eg Tajima)=== | |||
[[Korneliussen2013]] | |||
Revision as of 18:28, 2 October 2013
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
- -doSNP
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