vcf_filtering: VCF filtering using GATK

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

Description

This function filters VCF calls using GATK statistics

Usage

vcf_filtering(
  bin_path = "tools/gatk/gatk",
  bin_path2 = "tools/htslib/bgzip",
  bin_path3 = "tools/htslib/tabix",
  unfil_vcf = "",
  ref_genome = "",
  unfil_vcf_stats = "",
  contamination = "",
  segmentation = "",
  orientation_model = "",
  verbose = FALSE,
  output_dir = ""
)

Arguments

bin_path	REQUIRED Path to gatk binary. Default tools/gatk/gatk.
bin_path2	REQUIRED Path to bgzip binary. Default tools/htslib/bgzip.
bin_path3	REQUIRED Path to tabix binary. Default tools/htslib/tabix.
unfil_vcf	REQUIRED Path to unfiltered vcf file.
ref_genome	REQUIRED Path to reference genome fasta file.
unfil_vcf_stats	REQUIRED Path to unfiltered vcf file stats.
contamination	OPTIONAL Path to contamination table. Also requires segmentation.
segmentation	OPTIONAL Path to segments table. Also requires contamination.
orientation_model	OPTIONAL Path to orientation model generated using learn_orientation.
verbose	OPTIONAL Enables progress messages. Default False.
output_dir	OPTIONAL Path to the output directory.

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