ANGSD: Analysis of next generation Sequencing Data
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2d SFS Estimation: Difference between revisions
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Each run will generate 2 files of interest: '''pop1.saf,pop1.saf.pos''' and '''pop2.saf,pop2.saf.pos''' | Each run will generate 2 files of interest: '''pop1.saf,pop1.saf.pos''' and '''pop2.saf,pop2.saf.pos''' | ||
If we were interested in estimating the 1d sfs for each population we could do it like this using the [[EmOptim2]] program. | |||
<pre> | |||
emOptim2 pop1.saf 24 -P 24 >pop1.saf.sfs | |||
</pre> | |||
Revision as of 21:44, 12 March 2014
Angsd can estimate a 2d site frequency spectrum. This is an extension of the 1d site frequency spectrum method.
The method works by calculating population specific sample allele frequencies. A minor annoyance in the current implementation is that you will need to limit the analysis to the sites that has coverage in both population. This in effect means that you will need to do two passes for each population.
And is best explained by a full example.
Example
- Assume you have a 12 bamfiles for population in the file pop1.list
- Assume you have a 14 bamfiles for population in the file pop2.list
- Assume you have a fastafile containing the ancestral state in the anc.fa
- Assume we are only interested in chr1
Let's start by finding the positions for which we have data in population1 and population2
angsd -b pop1.list -anc anc.fa -r chr1: -P 10 -out pop1 angsd -b pop2.list -anc anc.fa -r chr1: -P 10 -out pop2
Each run will generate 2 files of interest: pop1.saf,pop1.saf.pos and pop2.saf,pop2.saf.pos
If we were interested in estimating the 1d sfs for each population we could do it like this using the EmOptim2 program.
emOptim2 pop1.saf 24 -P 24 >pop1.saf.sfs