plink_vcf_conversion: Convert VCF files to PLINK binary files

In imbs-hl/imbs: Collection of functions used at the IMBS

Description

Be sure the VCF file is well prepared!

Usage

plink_vcf_conversion(vcf.file, output.prefix, ..., build = "b37",
  plink.exec = "plink2", num.threads, memory)

Arguments

vcf.file	[string] The VCF file path.
output.prefix	[string] The basename of the new binary PLINK files.
...	[character] Additional arguments passed to PLINK.
build	[string] Human genome build code to split the X chromosome into pseudo-autosomal region and pure X. Default is 'b37' (alias 'hg19').
plink.exec	[string] Path of PLINK executable.
num.threads	[int] Number of CPUs usable by PLINK. Default is determined by SLURM environment variables and at least 1.
memory	[int] Memory for PLINK in Mb. Default is determined by minimum of SLURM environment variables SLURM_MEM_PER_CPU and num.threads * SLURM_MEM_PER_NODE and at least 5000.

Details

Based on the best practices on http://apol1.blogspot.de/2014/11/best-practice-for-converting-vcf-files.html. The procedure will take the VCF file and convert it to PLINK format. Be sure the VCF file is well prepared! See PLINK manual https://www.cog-genomics.org/plink/1.9/.

Value

Captured system output as character vector.

See Also

plink_normalize_vcf_conversion

vcf_normalization

imbs-hl/imbs documentation built on Sept. 6, 2019, 11:05 p.m.