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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| Line 19: | Line 19: | ||
===Genotype likelihoods=== | ===Genotype likelihoods=== | ||
; -GL 1 | ; -GL 1 | ||
same as in samtools [[ | same as in samtools [[Li2011]] | ||
; -GL 2 | ; -GL 2 | ||
same as in [[gatk]] | same as in [[gatk]] | ||
Revision as of 11:38, 29 June 2013
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 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