merge_bam_files: Merge multiple .bam files

In compbiomed/MetaScope: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data

Merge multiple .bam files

Description

This function merges .bam files. It first used the combined_header function to generate a combined header for all the files, reheaders the files, and then merges and sorts the .bam files. It is similar to the 'samtools merge' function, but it allows the .bam files to have different headers. It is not intended for direct use.

Usage

merge_bam_files(
  bam_files,
  destination,
  head_file = paste(destination, "_header.sam", sep = ""),
  quiet = TRUE
)

Arguments

bam_files	A list of file names for the .bam files to be merged.
destination	A file name and location for the merged .bam file.
head_file	A file name and location for the combined header file. Defaults to the destination. For example, 'example.bam' will be written as 'example.bam'.
quiet	Turns off most messages. Default is TRUE.

Value

This function merges .bam files and combines them into a single file. The function also outputs the new .bam filename.

compbiomed/MetaScope documentation built on April 1, 2024, 5:35 p.m.