merge_bams_samtools: Merge BAM files in directory

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

Merge BAM files in directory

Description

This function takes a BAM file and merges it with others found within a directory. This function is still Work In Progress (WIP).

Usage

merge_bams_samtools(
  bin_samtools = build_default_tool_binary_list()$bin_samtools,
  bams = "",
  output_name = "",
  verbose = TRUE,
  threads = 3,
  ram = 4,
  executor = make_unique_id("mergeBAMs"),
  task = "mergeBAMs",
  mode = "local",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bin_samtools	Path to samtools binary.
output_name	Output file name
verbose	Enables progress messages. Default False.
threads	Number of threads to use.Default 3.
bam	Path to the input bam file with the sequence.
bam_dir	Path to directory with BAM files to merge.

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