gl.read.vcf

-- a vcf file (works only for diploid data)

vcffile

verbose

switch to run the function once vcfR package is installed

installed

This function needs package vcfR. At the time of writing (August 2020) the package was no longer available from CRAN. To install the package check their github repository. <a href="https://github.com/knausb/vcfR">https://github.com/knausb/vcfR</a>. 
Once installed uncomment and run with installed=TRUE

Functions are provided that facilitate the import and analysis of
SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. The main focus is on data generated
by DarT (Diversity Arrays Technology). However, once SNP or related fragment
presence/absence data from any source is imported into a genlight object many
of the functions can be used. Functions are available for input and output of
SNP and silicodart data, for reporting on and filtering on various criteria
(e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency).
Advanced filtering is based on Linkage Disequilibrium and HWE (Hardy-Weinberg equilibrium). Other functions
are available for visualization after PCoA (Principle Coordinate Analysis), or to facilitate transfer of data
between genlight/genind objects and newhybrids, related, phylip, structure, faststructure packages.

Bernd Gruber

dartR

Importing and Analysing SNP and Silicodart Data Generated by
Genome-Wide Restriction Fragment Analysis

Arthur Georges

Peter J. Unmack

Oliver Berry

Lindsay V. Clark

Floriaan Devloo-Delva

gl.read.vcf function

This function needs package vcfR. At the time of writing (August 2020) the package was no longer available from CRAN. To install the package check their github repository. <a href='https://github.com/knausb/vcfR'>https://github.com/knausb/vcfR</a>. 
Once installed uncomment and run with installed=TRUE

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

Description

Usage

Arguments

Value