Converts a genlight object into vcf format

This function exports a genlight object into VCF format and save it into a file.

Usage

gl2vcf(
  x,
  plink_path = getwd(),
  outfile = "gl_vcf",
  outpath = tempdir(),
  snp_pos = "0",
  snp_chr = "0",
  chr_format = "character",
  pos_cM = "0",
  ID_dad = "0",
  ID_mom = "0",
  sex_code = "unknown",
  phen_value = "0",
  verbose = NULL
)

Arguments

x: Name of the genlight object containing the SNP data [required].
plink_path: Path of PLINK binary file [default getwd())].
outfile: File name of the output file [default 'gl_vcf'].
outpath: Path where to save the output file [default tempdir(), mandated by CRAN]. Use outpath=getwd() or outpath='.' when calling this function to direct output files to your working directory.
snp_pos: Field name from the slot loc.metrics where the SNP position is stored [default '0'].
snp_chr: Field name from the slot loc.metrics where the chromosome of each is stored [default '0'].
chr_format: Whether chromosome information is stored as 'numeric' or as 'character', see details [default 'character'].
pos_cM: A vector, with as many elements as there are loci, containing the SNP position in morgans or centimorgans [default '0'].
ID_dad: A vector, with as many elements as there are individuals, containing the ID of the father, '0' if father isn't in dataset [default '0'].
ID_mom: A vector, with as many elements as there are individuals, containing the ID of the mother, '0' if mother isn't in dataset [default '0'].
sex_code: A vector, with as many elements as there are individuals, containing the sex code ('male', 'female', 'unknown') [default 'unknown'].
phen_value: A vector, with as many elements as there are individuals, containing the phenotype value. '1' = control, '2' = case, '0' = unknown [default '0'].
verbose: Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity].

Details

This function requires to download the binary file of PLINK 1.9 and provide its path (plink_path). The binary file can be downloaded from: https://www.cog-genomics.org/plink/

The chromosome information for unmapped SNPS is coded as 0. Family ID is taken from x$pop Within-family ID (cannot be '0') is taken from indNames(x) Variant identifier is taken from locNames(x)

References

Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., ... & 1000 Genomes Project Analysis Group. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156-2158.

Author

Custodian: Luis Mijangos (Post to https://groups.google.com/d/forum/dartr)

Examples

if (FALSE) {
require("dartR.data")
gl2vcf(platypus.gl,snp_pos='ChromPos_Platypus_Chrom_NCBIv1',
 snp_chr = 'Chrom_Platypus_Chrom_NCBIv1')
}