BamUtil: mergeBam: Difference between revisions
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== 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. | rgMergeBam merges multiple sorted BAM files into one BAM file like 'samtools merge' command, but merges BAM headers. | ||
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=== Usage=== | === Usage=== | ||
<pre> | <pre> | ||
rgMergeBam [-v] [-l listFile] [-o outFile] [-L logFile] [inputBAMfile1] [inputBAMfile2] ... | |||
Required arguments: | Required arguments: | ||
Revision as of 21:42, 1 November 2010
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] [-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
