estimate_contamination_parallel: 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_parallel(
  bin_path = "tools/gatk/gatk",
  bam_dir = "",
  germ_pattern = "GL",
  patient_id = "",
  db = "",
  interval = "",
  verbose = FALSE,
  output_dir = "",
  threads = 3
)

Arguments

bin_path	REQUIRED Path to gatk binary. Default tools/gatk/gatk.
bam_dir	REQUIRED Path to directory with BAM files
germ_pattern	REQUIRED Pattern to match normal samples.
patient_id	REQUIRED Pattern to match patient specific samples.
db	REQUIRED Path to vcf with known variants.
interval	REQUIRED Path to vcf with intervals to analyze.
verbose	OPTIONAL Enables progress messages. Default False.
output_dir	OPTIONAL Path to the output directory.
threads	OPTIONAL Number of threads to use. Default 3.

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