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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Currently there is not publication for angsd. However, many of the method implimented here are published. | Currently there is not publication for angsd. However, many of the method implimented here are published. | ||
==Methods== | |||
===Allele estimation=== | |||
allele estimation from genotype likelihoods | allele estimation from genotype likelihoods | ||
;- doMaf | ;- doMaf | ||
[[kim2011]] | [[kim2011]] | ||
===SNP calling=== | |||
SNP calling based on genotype likelihoods | SNP calling based on genotype likelihoods | ||
; -doSNP | |||
[[kim2011]] | [[kim2011]] | ||
Genotype likelihoods | ===Genotype likelihoods=== | ||
; -GL 1 | ; -GL 1 | ||
same as in samtools [[Li2010]] | same as in samtools [[Li2010]] | ||
| Line 18: | Line 21: | ||
same as in [[soapSNP]] | same as in [[soapSNP]] | ||
; -GL 4 | ; -GL 4 | ||
same as in [[kim2011]] | |||
Revision as of 13:34, 24 September 2012
Currently there is not publication for angsd. However, many of the method implimented here are published.
Methods
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