plink_normalize_vcf_conversion: Normalize and convert VCF files to PLINK binary files

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

Description

Normalize and convert VCF files to PLINK binary files

Usage

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

Arguments

vcf.file	[string] The VCF file path.
ref.file	[string] A human reference genome fasta file to normalize indels against.
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').
bcftools.exec	[string] Path of bcftools executable.
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, strip the variant IDs, split multi-allelic sites into bi-allelic sites, assign names to make sure indels will not become ambiguous, and finally convert to PLINK format. See PLINK manual https://www.cog-genomics.org/plink/1.9/.

Value

Captured system output as character vector.

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