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.
Thetas,Tajima,Neutrality tests: Difference between revisions
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To estimate the thetats do: | To estimate the thetats do: | ||
<code> | <code> | ||
./angsd [other input] -realSFS 1 -doThetas 1 -prior prior.sfs.ml | ./angsd [other input] -realSFS 1 -doThetas 1 -prior prior.sfs.ml | ||
</code> | </code> | ||
The prior is an estimate of the .sfs which can be found using the [RealSFS] method in angsd | The prior is an estimate of the .sfs which can be found using the [RealSFS] method in angsd | ||
The output is a file called .thetas.gz | The output is a file called .thetas.gz | ||
Revision as of 01:53, 18 December 2012
Angsd can estimate the Tajimas D and other neutrality test. Method works by using the posterior allele frequencies for every site, and uses these for calculating different per-site estimates of theta.
Due to the linearity the population scaled mutation rate is therefore the sum of the per-site estimates
To estimate the thetats do:
./angsd [other input] -realSFS 1 -doThetas 1 -prior prior.sfs.ml
The prior is an estimate of the .sfs which can be found using the [RealSFS] method in angsd The output is a file called .thetas.gz To perform the Tajimas D and other related neutralitet tests you should feed the .thetas.gz file into a seperate program called calcstat which can be found in the misc dir of the sourcecode
./calcStat24 -tinput file.thetas.gz -step 50000 -win 50000