BamUtil: mergeBam
From Genome Analysis Wiki
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
RGAMerge [-v] [-l listFile] [-o outFile] [-L logFile] [inputBAMfile1] [inputBAMfile2] ...
Required arguments:
-l listFile : File containing RG tags including [BAM] [ID] [SM] [LB]
-o outFile : output BAM file name
Optional arguments:
-L logFile : log file name. default is listFile.log
-v : turn on verbose mode
