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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(Created page with "Currently there is not publication for angsd. However, many of the method implimented here are published. **Methods** allele estimation from genotype likelihoods ;- doMaf ...") |
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allele estimation from genotype likelihoods | allele estimation from genotype likelihoods | ||
;- doMaf | ;- doMaf | ||
[[ | [[kim2011]] | ||
SNP calling based on genotype likelihoods | SNP calling based on genotype likelihoods | ||
[[ | [[kim2011]] | ||
Genotype likelihoods | Genotype likelihoods | ||
; -GL 1 | ; -GL 1 | ||
same as in samtools [[ | same as in samtools [[Li2010]] | ||
; -GL 2 | ; -GL 2 | ||
same as in | same as in [[gatk]] | ||
; -GL 3 | ; -GL 3 | ||
same as in | same as in [[soapSNP]] | ||
; -GL 4 | ; -GL 4 | ||
Revision as of 12:28, 24 September 2012
Currently there is not publication for angsd. However, many of the method implimented here are published.
- Methods**
allele estimation from genotype likelihoods
- - doMaf
SNP calling based on genotype likelihoods kim2011
Genotype likelihoods
- -GL 1
same as in samtools Li2010
- -GL 2
same as in gatk
- -GL 3
same as in soapSNP
- -GL 4