call_vep_maf: Variant annotation in MAF format

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

Description

This function annotates a VCF file using VEP, and then generates a corresponding MAF file for it.

Usage

call_vep_maf(
  bin_path = "tools/vcf2maf/vcf2maf.pl",
  vep_dir = "tools/ensembl/vep",
  vep_data = "~/.vep",
  vcf = "",
  verbose = FALSE,
  output_dir = "",
  patient_id = "",
  normal_id = "",
  ref_genome = "",
  tumour_id = "",
  threads = 3
)

Arguments

bin_path	REQUIRED Path to vcf2maf executable. Default path tools/vcf2maf/vcf2maf.pl
vep_dir	REQUIRED Path to VEP executable directory. Default path tools/ensembl/vep
vep_data	REQUIRED Path to VEP data directory. Default path ~/.vep
vcf	REQUIRED Path to vcf to annotate.
verbose	OPTIONAL Extra verbose. Default FALSE.
output_dir	OPTIONAL Directory to output
patient_id	OPTIONAL Patient ID. If not given the name of the first sample in alphanumerical order will be used.
normal_id	OPTIONAL Normal ID
ref_genome	REQUIRED Path to reference genome fasta file.
tumour_id	OPTIONAL Tumour ID in VCF. If not given file name will be used.
threads	OPTIONAL Number of threads

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