call_variants: Variant calling of Somatic and Germline (MuTECT2, Platypus...

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

Description

This function calls somatic and germline mutations, in previously pre-processed sequencing data. This function takes a path to a directory with BAM files and a patients ID. Then it subsets all BAM files specific to the patient, identifying between cancer and normal Samples using the germline identifier. Afterwards, it calls the MuTECT2 somatic variant caller, to indentify somatics variants, and Platypus genotyper all variants found in the samples. Finally, it calls Varant Effect Predictor (VEP) and annotates all the variants.

Usage

call_variants(
  bin_path = "tools/gatk/gatk",
  bin_path2 = "tools/bcftools/bcftools",
  bin_path3 = "tools/htslib/bgzip",
  bin_path4 = "tools/htslib/tabix",
  bin_path5 = "tools/platypus/Platypus.py",
  bin_path6 = "tools/ensembl-vep/vep",
  bin_path7 = "tools/strelka-2.9.10/build/bin/configureStrelkaGermlineWorkflow.py",
  bin_path8 = "tools/manta-1.6.0/build/bin/configManta.py",
  bin_path9 = "tools/svaba/bin/svaba",
  bam_dir = "",
  patient_id = "",
  germ_pattern = "GL",
  ref_genome = "",
  germ_resource = "",
  pon = "",
  output_dir = "",
  region_bed = "",
  chr_filter = "canonical",
  db = "",
  interval = "",
  targets = "",
  orientation = TRUE,
  resources = "",
  info_key = "CNN_2D",
  snp_tranche = 99.95,
  indel_tranche = 99.4,
  threads = 3,
  verbose = FALSE,
  targeted = TRUE,
  validate_id = TRUE
)

Arguments

bin_path	REQUIRED Path to gatk binary. Default tools/gatk/gatk.
bin_path2	REQUIRED Path to bcftools binary. Default tools/bcftools/bcftools.
bin_path3	REQUIRED Path to bgzip binary. Default tools/htslib/bgzip.
bin_path4	REQUIRED Path to tabix binary. Default tools/htslib/tabix.
bin_path5	REQUIRED Path to platypus binary. Default tools/platypus/Platypus.py.
bin_path6	REQUIRED Path to vep binary binary. tools/ensembl-vep/vep
bin_path7	REQUIRED Path to Strelka Germline Workflow binary. tools/strelka-2.9.10/build/bin/configureStrelkaGermlineWorkflow.py
bin_path8	REQUIRED Path to Manta binary. tools/manta-1.6.0/build/bin/configManta.py
bin_path9	REQUIRED Path to svaba binary. tools/svaba/bin/svaba
bam_dir	REQUIRED Path to directory with BAM files.
patient_id	REQUIRED Patient ID to analyze. Has to be in file names to subselect samples.
germ_pattern	REQUIRED Pattern used to identify germline samples. Ex GL
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.
chr_filter	OPTIONAL Chromosomes to analyze. canonical/autosomal/all or a list of chromosomes
db	OPTIONAL Path to vcf with common variants. Used for contamination estimation.
interval	OPTIONAL Path to interval for common variants to analyze. Used for contamination estimation.
targets	OPTIONAL Path to BED file with capture targets.
orientation	OPTIONAL Generate a read orientation model to filter variants. Default TRUE
info_key	OPTIONAL Annotation column to select. Default CNN_D2
snp_tranche	OPTIONAL SNP tranche filter value. Default 99.95
indel_tranche	OPTIONAL Indel tranche filter value. Default 99.44
threads	OPTIONAL Number of threads. Default 3
verbose	OPTIONAL Enables progress messages. Default False.
targeted	OPTIONAL Sequencing method Exome/Targeted. Default TRUE
validate_id	OPTIONAL Validate patient_id in BAM dir. Default TRUE.
output_name	OPTIONAL Name for the output. If not given the name of one of the samples will be used.

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