annotate_strelka_vep: Create Read Orientation Model for Mutect2 Filter

In TearsWillFall/ULPwgs: An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems

Create Read Orientation Model for Mutect2 Filter

Description

This function creates read orientation model for mutect2 filtering

Usage

annotate_strelka_vep(
  bin_vep = build_default_tool_binary_list()$bin_vep,
  bin_bgzip = build_default_tool_binary_list()$bin_bgzip,
  bin_tabix = build_default_tool_binary_list()$bin_tabix,
  cache_vep = build_default_cache_list()$cache_vep,
  vcf = NULL,
  patient_id = NULL,
  tumour_id = NULL,
  normal_id = NULL,
  fmt = "vcf",
  tabulate = TRUE,
  type = "snv",
  chromosomes = NULL,
  ...
)

Arguments

bin_vep	REQUIRED Path to VEP binary.
bin_bgzip	REQUIRED Path to bgzip binary.
bin_tabix	REQUIRED Path to tabix binary.
vcf	REQUIRED Path to VCF file.
vep_cache	REQUIRED Path to vep cache location.
compress	OPTIONAL Generate a compressed VCF
output_name	OPTIONAL Name of output file
clean	OPTIONALRemove extra files.
output_dir	OPTIONAL Path to the output directory.
threads	OPTIONAL Number of threads to split the work. Default 4
ram	OPTIONAL RAM memory to asing to each thread. Default 4
verbose	OPTIONAL Enables progress messages. Default False.
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
executor_id	Task EXECUTOR ID. Default "recalCovariates"
task_name	Task name. Default "recalCovariates"
time	OPTIONAL If batch mode. Max run time per job. Default "48:0:0"
update_time	OPTIONAL If batch mode. Job update time in seconds. Default 60.
wait	OPTIONAL If batch mode wait for batch to finish. Default FALSE
hold	OPTIONAL HOld job until job is finished. Job ID.

TearsWillFall/ULPwgs documentation built on April 18, 2024, 3:45 p.m.