generate_reordering_for_vcf: Generate reordering information for a VCF file

In nwvankuren/gwplotting: Utilities for plotting statistics from genome-wide analyses

Generate reordering information for a VCF file

Description

This function will produce two files that you can use in conjunction with PLINK to reorder your VCF according to chromosome assignments.

Usage

generate_reordering_for_vcf(vcf, scaffold_lengths, assignments, species, out)

Arguments

vcf	The name of the VCF file that you want to reorder.
scaffold_lengths	Draft genome scaffold lengths.
assignments	Name of the file containing the reordering information.
species	The abbreviation for the species assembly you ordered to.
out	Prefix of the files to write to.

Value

Nothing. Produces two files: out.exclude.txt and out.reordering.txt for use with PLINK and your original VCF file.

nwvankuren/gwplotting documentation built on July 5, 2024, 4:24 p.m.