new_tg_summary_metrics_bam_picard: Generate BAM Summary for Targeted data

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

Generate BAM Summary for Targeted data

Description

Generate BAM Summary for Targeted data

Usage

new_tg_summary_metrics_bam_picard(
  bin_picard = build_default_tool_binary_list()$bin_picard,
  bam = NULL,
  ref_genome = build_default_reference_list()$HG19$reference$genome,
  bi = build_default_reference_list()$HG19$panel$PCF_V3$intervals$bi,
  ti = build_default_reference_list()$HG19$panel$PCF_V3$intervals$ti,
  ...
)

Arguments

bin_picard	Path to bwa executable. Default path tools/samtools/samtools.
bam	Path to the input file with the sequence.
bi	Bait capture target interval for panel data. Interval format.
ti	Primary target intervals for panel data. Interval format.
output_dir	Path to the output directory.
verbose	Enables progress messages. Default False.
ram	RAM memory to use in GB. Default 4.
tmp_dir	Path to TMP directory. Default .
executor_id	OPTIONAL Task executor name. Default "recalCovariates"
task_name	OPTIONAL 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.