gl2vcf {dartR.base}

Converts a genlight object into vcf format

Description

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

Usage

gl2vcf(
  x,
  plink.bin.path = getwd(),
  outfile = "gl_vcf",
  outpath = NULL,
  snp.pos = "0",
  snp.chr = "0",
  chr.format = "character",
  pos.cM = "0",
  ID.dad = "0",
  ID.mum = "0",
  sex.code = "unknown",
  phen.value = "0",
  verbose = NULL
)

Arguments

x

Name of the genlight object containing the SNP data [required].

plink.bin.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 global working directory or if not specified, tempdir()].

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.mum

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.bin.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)

Value

returns no value (i.e. NULL)

Author(s)

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

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.

See Also

Other linker: gl2bayesAss(), gl2bayescan(), gl2bpp(), gl2demerelate(), gl2eigenstrat(), gl2faststructure(), gl2gds(), gl2genalex(), gl2genepop(), gl2geno(), gl2gi(), gl2hiphop(), gl2phylip(), gl2plink(), gl2related(), gl2sa(), gl2structure(), gl2treemix()

Examples

## Not run: 
#this example needs plink installed to work
require("dartR.data")
gl2vcf(platypus.gl,snp.pos='ChromPos_Platypus_Chrom_NCBIv1',
 snp.chr = 'Chrom_Platypus_Chrom_NCBIv1')

## End(Not run)