ANGSD: Analysis of next generation Sequencing Data
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Thetas,Tajima,Neutrality tests: Difference between revisions
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Angsd can estimate the Tajimas D and other neutrality test. | 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. | 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 | Due to the linearity the population scaled mutation rate is therefore the sum of the per-site estimates | ||
To estimate the thetats do: | |||
<code> | |||
./angsd [other input] -realSFS 1 -doThetas 1 -prior prior.sfs.ml | |||
</code> | |||
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 | |||
<code> | |||
./calcStat24 -tinput file.thetas.gz -step 50000 -win 50000 | |||
</code> | |||
Revision as of 02:53, 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