call_vep: Predict variant effect using VEP

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

Description

This function predicts the effect of variant found in a VCF file

Usage

call_vep(
  bin_path = "tools/ensembl-vep/vep",
  bin_path2 = "tools/htslib/bgzip",
  bin_path3 = "tools/htslib/tabix",
  vcf = "",
  output_name = "",
  verbose = FALSE,
  output_dir = "",
  threads = 3
)

Arguments

bin_path	Path to bcftools binary. Default tools/ensembl-vep/vep.
bin_path2	Path to bgzip binary. Default tools/htslib/bgzip.
bin_path3	Path to bgzip binary. Default tools/htslib/tabix.
vcf	Path to vcf file.
output_name	Name used for output files. If not given the vcf file name will be used
verbose	Enables progress messages. Default False.
output_dir	Path to the output directory.
threads	Number of threads to use. Default 3.

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