pvdiv_subset_popgenome: Get GFF subsets

In Alice-MacQueen/switchgrassGWAS: Genome Wide Association on Panicum virgatum

Description

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.

Usage

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.

Alice-MacQueen/switchgrassGWAS documentation built on Jan. 23, 2022, 7:55 p.m.