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Converts a genlight object into vcf format

Source: R/gl2vcf.r
gl2vcf.Rd

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].

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].

Value

returns no value (i.e. NULL)

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)

#' Note that if names of populations or individuals contain spaces, they are replaced by an underscore "_".

If you like to use chromosome information when converting to plink format and your chromosome names are not from human, you need to change the chromosome names as 'contig1', 'contig2', etc. as described in the section "Nonstandard chromosome IDs" in the following link: https://www.cog-genomics.org/plink/1.9/input

Note that the function might not work if there are spaces in the path to the plink executable.

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) { # \dontrun{
require("dartR.data")
gl2vcf(platypus.gl,snp_pos='ChromPos_Platypus_Chrom_NCBIv1',
 snp_chr = 'Chrom_Platypus_Chrom_NCBIv1')
} # }