BamUtil: mergeBam

RGMergeBAM : Merge 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

 rgMergeBam [-v]options) --list=<RGAListFile> --out=<outBamFile>
rgMergeBam [-v] [-L logFile] [-l listFile] [-o outFile]

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