BamUtil: mergeBam

Overview of the rgMergeBam function of bamUtil

The rgMergeBam option on the bamUtil executable merges multiple BAM files appending ReadGroup IDs.

rgMergeBam merges multiple sorted BAM files into one BAM file like 'samtools merge' command, but merges BAM headers.

• Checks that the HD and SQ tags are identical across the BAM files
• Adds @RG headers from a tabular input file containing the fields' info
• Adds RG:Z:[RGID] tag for each record based on the source BAM file
• Ensures that the headers are identical across the input files and that input/output BAM records are sorted

Usage

./bam rgMergeBam [-v] [--log logFile] --list <listFile> --out <outFile>

Parameters

Required parameters :
--out/-o : Output BAM file (sorted)
--list/-l : RGAList File. Tab-delimited list consisting of following columns (with headers):
	BAM* : Input BAM file name to be merged
	ID* : Unique read group identifier
	SM* : Sample name
	LB : Library name
	DS : Description
	PU : Platform unit
	PI : Predicted median insert size
	CN : Name of sequencing center producing the read
	DT : Date the rn was produced
	PL : Platform/technology used to produce the read
	* (Required fields)
Optional parameters : 
--log/-L : Log file
--verbose/-v : Turn on verbose mode