call_mutect2: Variant calling using MuTECT2

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

Description

This function calls somatic variants in a pair of tumor-normal matched samples, or just in a tumor sample if no matched sample is not available.

Usage

call_mutect2(
  region = "",
  bin_path = "tools/gatk/gatk",
  tumor_bam = "",
  normal_bam = "",
  ref_genome = "",
  germ_resource = "",
  pon = "",
  output_dir = "",
  output_name = "",
  verbose = FALSE,
  orientation = TRUE,
  mnps = TRUE
)

Arguments

region	Region to analyze. Optional
bin_path	Path to fastQC executable. Default path tools/gatk/gatk.
tumor_bam	Path to tumor bam file.
normal_bam	Path to germline bam file.
ref_genome	Path to reference genome fasta file.
germ_resource	Path to germline resources vcf file.
pon	Optional Path to panel of normal.
output_dir	Path to the output directory.
output_name	OPTIONAL Name for the output. If not given the name of one of the samples will be used.
verbose	Enables progress messages. Default False.
mnps	Report MNPs in vcf file.

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