vcf_sort: Sort VCF file

In TearsWillFall/variantCall: An implementation of a wrapper for variant calling using MuTECT2 and Platypus GNU/Unix based systems

Description

This function takes a VCF file and sorts it genomic order

Usage

vcf_sort(
  bin_path = "tools/bcftools/bcftools",
  vcf = "",
  verbose = FALSE,
  output_dir = "",
  ram = 4,
  tmp_dir = ""
)

Arguments

bin_path	Required Path to bcftools binary. Default tools/bcftools/bcftools.
vcf	Required Path to VCF file to sort.
verbose	Optional Enables progress messages. Default False.
output_dir	Optional Path to the output directory. Default working directory.
ram	Required RAM in GB to allocate sorting. Default 4Gb.
tmp_dir	Optional Path to tmp file directory.

TearsWillFall/variantCall documentation built on Oct. 15, 2021, 8:51 p.m.