call_mutect2_parallel: Variant calling using MuTECT2 on parallel per genomic region

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_parallel(
  bin_path = "tools/gatk/gatk",
  bin_path2 = "tools/bcftools/bcftools",
  bin_path3 = "tools/htslib/bgzip",
  bin_path4 = "tools/htslib/tabix",
  tumor_bam = "",
  normal_bam = "",
  bam_dir = "",
  patient_id = "",
  germ_pattern = "GL",
  ref_genome = "",
  germ_resource = "",
  pon = "",
  output_dir = "",
  region_bed = "",
  db = "",
  interval = "",
  threads = 3,
  verbose = FALSE,
  chr_filter = "canonical",
  orientation = TRUE,
  validate_id = TRUE
)

Arguments

bin_path	REQUIRED Path to gatk binary. Default path tools/gatk/gatk.
bin_path2	REQUIRED Path to bcftools binary. Default path tools/bcftools/bcftools.
bin_path3	REQUIRED Path to tabix binary. Default path tools/htslib/tabix.
bin_path4	REQUIRED Path to bgzip binary. Default path tools/htslib/bgzip.
tumor_bam	OPTIONAL Path to tumor bam file/s.
normal_bam	OPTIONAL Path to germline bam file/s.
bam_dir	OPTIONAL Path to bam_dir. Only if tumor_bam and/or normal_bam not given.
patient_id	OPTIONAL Patients ID to identify project with. Otherwise name of tumor sample will be used.
germ_pattern	OPTIONAL Identifier for normal samples. Default GL. Only used when bam_dir is given.
ref_genome	REQUIRED Path to reference genome fasta file.
germ_resource	REQUIRED Path to germline resources vcf file.
pon	OPTIONAL Path to panel of normal.
output_dir	OPTIONAL Path to the output directory.
region_bed	REQUIRED Path to bed file with regions to analyze.
db	OPTIONAL Path to vcf with known variants for contamination estimation.
interval	OPTIONAL Path to vcf with intervals to analyze contamination.
threads	OPTIONAL Number of threads. Default 3
verbose	OPTIONAL Enables progress messages. Default False.
chr_filter	OPTIONAL Chromosomes to analyze. canonical/autosomal/all or a list of chromosomes
orientation	OPTIONAL Generate a read orientation model to filter variants. Default False
validate_id	OPTIONAL Validate patient_id in BAM dir. Default TRUE

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