gl.read.vcf {dartR.base}

Converts a vcf file into a genlight object

Description

This function needs package vcfR, please install it. The converted genlight object does not have individual metrics. You need to add them 'manually' to the other$ind.metrics slot.

Usage

gl.read.vcf(vcf.file, verbose = NULL)

Arguments

vcf.file

A vcf file (works only for diploid data) [required].

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].

Value

A genlight object.

Author(s)

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

See Also

Other io: gl.load(), gl.read.csv(), gl.read.dart(), gl.read.fasta(), gl.read.silicodart(), gl.save(), gl.write.csv(), utils.read.dart()

Examples

# you need to provide the path to the vcf file
#obj <- gl.read.vcf("yourvcffile.vcf", package='dartR.data'))