estimate_contamination: VCF contamination estimation using GATK

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

Description

This function estimates sample contamination for further variant filtering

Usage

estimate_contamination(
  pileup_table_tumor = "",
  bin_path = "tools/gatk/gatk",
  pileup_table_normal = "",
  verbose = FALSE,
  output_dir = ""
)

Arguments

pileup_table_tumor	REQUIRED Path to pileup_table for tumor sample generated using pileup_summary
bin_path	REQUIRED Path to gatk binary. Default tools/gatk/gatk.
pileup_table_normal	OPTIONAL Path to pileup_table for matched normal sample generated using pileup_summary
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.