skyclub3/vcf2sfs

R functions for calculating site frequency spectrum (SFS) or joint SFS of more than one population from a VCF file.

vcf2sfs

R functions for calculating site frequency spectrum (SFS) or joint SFS of more than one population from a VCF file.

Input and output formats

The main transformation function is vcf2dadi(). It requires two input files. One is the VCF file, and the other is a so-called popmap file. The popmap file is a tab-delimited two-column text file. Its first column specifies the IDs of the individuals included in the VCF file (the individuals should be arranged in the same order as in the VCF file; the IDs do not need to be the same as those in the header line of the VCF file). The second column specifies the populaton ID of each individual (coded in integers). The output of vcf2dadi() is in dadi format. But there are extra functions to transform dadi format into fastSimCoal format.

Note!

The function vcf2dadi() parses the GT fields of the sample columns. Therefore, in order for this function to work, the VCF file must contain the GT fields and they must be placed at the beginning of each sample column. This can be verified by looking at the 9th column (the FORMAT column) of the VCF file. Some VCF files generated using GATK do not have the GT fields, hence unable to make use of this function. Future update of this function is expected to overcome this limitation.

Instructions

For more detailed instructions, please see "readme.r"

Example

I provide an example VCF file and an example popmap file. The dataset includes 197 individuals belonging to 11 populations.

To create the SFS of Population 1, you simply need to run:

source("vcf2sfs.r")

vcf2dadi("example.vcf","example_popmap.txt","pop1.fs",1)

To create the joint SFS between Populations 1 and 2:

vcf2dadi("example.vcf","example_popmap.txt","pop1_pop2.fs",c(1,2))

To create the joint SFSs for all possible pairs or populations:

popPairs<-combn(1:11,2)

for(i in 1:ncol(popPairs))

vcf2dadi("example.vcf","example_popmap.txt",sprintf("pop%d_pop%d.fs",popPairs[1,i],popPairs[2,i]),popPairs[,i])

Citation

Liu S, Ferchaud AL, Groenkjaer P, Nygaard R, Hansen MM (2018) Genomic parallelism and lack thereof in contrasting systems of three-spine sticklebacks. Molecular Ecology, Vol. 27 (in press).