concatenate_bams: Concatenate 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

Concatenate BAM files in directory.

Description

This function takes a BAM file and merges it with others found within a directory. The ouput file is a non-sorted bam file

Usage

concatenate_bams(
  bin_samtools = build_default_tool_binary_list()$bin_samtools,
  bams = "",
  output_name = "",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  threads = 3
)

Arguments

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.