vcf_bcftools: Variant calling using bcftools

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

Description

This function calls variants in a sample.

Usage

vcf_bcftools(
  region = "",
  bin_path = "tools/bcftools/bcftools",
  bam = "",
  ref_genome = "",
  output_dir = "",
  verbose = FALSE
)

Arguments

region	Region to analyze. Optional
bin_path	Path to fastQC executable. Default path tools/gatk/gatk.
bam	Path to bam file.
ref_genome	Path to reference genome fasta file.
output_dir	Path to the output directory.
verbose	Enables progress messages. Default False.

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