gl.read.vcf: Converts a vcf file into a genlight object

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Converts a vcf file into a genlight object

Description

This function needs package vcfR, please install it.

Usage

gl.read.vcf(vcffile, ind.metafile = NULL, verbose = NULL)

Arguments

vcffile	A vcf file (works only for diploid data) [required].
ind.metafile	Optional file in csv format with metadata for each individual (see details for explanation) [default NULL].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity].

Details

The ind.metadata file needs to have very specific headings. First a heading called id. Here the ids have to match the ids in the dartR object. The following column headings are optional. pop: specifies the population membership of each individual. lat and lon specify spatial coordinates (in decimal degrees WGS1984 format). Additional columns with individual metadata can be imported (e.g. age, gender).

Value

A genlight object.

Author(s)

Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)

Examples

## Not run: 
obj <- gl.read.vcf(system.file('extdata/test.vcf', package='dartR'))

## End(Not run)

dartR documentation built on April 4, 2025, 12:23 a.m.