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.
ANGSD: Difference between revisions
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example of allele frequency estimated from genotype likelihoods with bam files as input | example of allele frequency estimated from genotype likelihoods with bam files as input using 10 threads | ||
<code lang=sh> | <code lang=sh> | ||
./angsd -out outFileName -bam bam.filelist -GL 1 -doMaf 2 -doMajorMinor 1 | ./angsd -out outFileName -bam bam.filelist -GL 1 -doMaf 2 -doMajorMinor 1 -nThreads 10 | ||
</code> | </code> | ||
Revision as of 13:38, 19 June 2012
About
ANGSD is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. All methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data. The software is written in C++ and can handle thousands of samples
Overview of input and intermediary data
The input and intermediary data structures of angsd. <classdiagram type="dir:LR"> [sequence data]->[genotype;likelihoods] [genotype;likelihoods]->[genotype;probabilities] [sequence files|bam files;SOAP files{bg:orange}]->[sequence data] [glf files|glfv3;soapSNP{bg:orange}]->[genotype;likelihoods] [genotype prob|beagle output{bg:orange}]->[genotype;probabilities] </classdiagram>
Analysis from sequencing data
<classdiagram> // [input|bam files;SOAP files{bg:orange}]->[sequence data]
[sequence data]->[output|summary stats;phat estimates;error estimates{bg:blue}]
</classdiagram>
Analysis from genotype likelihoods
<classdiagram> //[input data|glf files{bg:orange}]->[genotype;likelihoods] [genotype;likelihoods]->[output|glf files;beagle files;MAF estimates;MAF associations;SNP Calling;realSFS;error estimates;Inbreeding{bg:blue}]
</classdiagram>
Analysis from genotype probabilities
<classdiagram> //[input data|beagle output{bg:orange}]->[genotype;probabilities] [genotype;probabilities]->[output|genotype calling;MAF estimates;associations{bg:blue}]
</classdiagram>
Synopsis
./angsd [OPTIONS]
example of allele frequency estimated from genotype likelihoods with bam files as input using 10 threads
./angsd -out outFileName -bam bam.filelist -GL 1 -doMaf 2 -doMajorMinor 1 -nThreads 10