Get GFF subsets

Prepare a subset of the P. virgatum VCF file to be used in the PopGenome R package. Given a VCF subset (created using VCFtools or some other commandline program), this function will make a GFF and VCF folder in the path, if they do not already exist, and place the VCF subset in the correct format in the VCF folder, and the GFF subset in the correct format in the GFF folder. These files can then be read into the R package PopGenome.

pvdiv_subset_popgenome(path, filename, seqid, start, end)

Arguments

path

file.path() or character string. Path to the VCF file subset.

filename

Character string. VCF subset filename

seqid

Character string. name of the chromosome or scaffold; here, of Panicum virgatum.

start

Integer. Start position of the feature, with sequence numbering starting at 1.

end

Integer. End position of the feature, with sequence numbering starting at 1.