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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==Methods== | ==Methods== | ||
===Maf estimation from counts of alleles=== | ===Maf estimation from counts of alleles=== | ||
-cutoff | , -cutoff | ||
[[Li2010]] | [[Li2010]] | ||
Revision as of 19:36, 23 October 2012
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