vcf_to_plink: Convert VCF to PLINK

In RajLabMSSM/echoLD: echoverse module: LD downloading and processing

Convert VCF to PLINK

Description

Convert a Variant Call File (VCF) to PLINK format.

Usage

vcf_to_plink(
  vcf,
  output_prefix = NULL,
  bcftools_path = NULL,
  make_bed = TRUE,
  recode = TRUE,
  verbose = TRUE
)

Arguments

vcf	Specify full name of .vcf or .vcf.gz file.
output_prefix	Specify prefix for output files.
bcftools_path	Path to bedtools executable. If NULL, will automatically be downloaded with find_executables_remote.
make_bed	Create a new binary fileset. Unlike the automatic text-to-binary converters (which only heed chromosome filters), this supports all of PLINK's filtering flags.
recode	Create a new text fileset with all filters applied.
verbose	Print messages.

Examples

vcf <- system.file("extdata", "BST1.1KGphase3.vcf.bgz",
    package = "echodata")
paths <- vcf_to_plink(vcf = vcf)

RajLabMSSM/echoLD documentation built on May 12, 2024, 3:23 a.m.