2d SFS Estimation

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 populations. 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

# as always you can add -minMapQ 1 and -minQ 20 to only keep high quality data.
angsd -GL 1 -b pop1.list -anc anc.fa -r chr1: -P 10 -out pop1
angsd -GL 1 -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 realSFS program. (See more on page )

realSFS pop1.saf 24 -P 24 >pop1.saf.sfs
realSFS pop2.saf 28 -P 24 >pop2.saf.sfs
#first argument is saf file, second argument is the number of chromosomes, -P 24 is the number of cores we want to use

Now we find the positions that occurs both in population1 and population2 using the uniq POSIX program.

cat pop1.saf.pos pop2.saf.pos|sort|uniq -d|sort -k1,1 >intersect.txt

And now we redo the angsd sample allelefrequence calculation by conditioning on the sites that occur in both populations

# as always you can add -minMapQ 1 and -minQ 20 to only keep high quality data.
angsd -GL 1 -b pop1.list -anc anc.fa -r chr1: -P 10 -out pop1 -sites intersect.txt
angsd -GL 1 -b pop2.list -anc anc.fa -r chr1: -P 10 -out pop2 -sites intersect.txt

Notice that the last 2 commands will overwrite the: pop1.saf,pop1.saf.pos and pop2.saf,pop2.saf.pos files.

And we now estimate the joint site frequency spectra by using the realSFS program

realSFS 2dsfs pop1.saf pop2.saf  24 28 -P 24 >2dsfs.sfs

The output is then located in a nice matrix format in the file: 2dsfs.sfs. Good luck visualising it, some people are using dadi, we have been using heat maps in R.