Difference between revisions of "BamUtil: splitBam"
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Revision as of 17:47, 16 January 2012
Overview of the splitBam function of bamUtil
The splitBam option on the bamUtil executable split a BAM file into multiple BAM files based on ReadGroup according to the following details.
- Creates multiple output files named [outprefix].[RGID].bam, for each ReadGroup ID (RGID) existing in the bam file
- Headers are a copy of the original file, removing @RG and @PG headers where IDs match with the other ReadGroup IDs.
- Copy each of the original file's BAM record to one of the output file where the ReadGroup ID matches
Usage
Usage : ./bam splitBAM [-v] -i <inputBAMFile> -o <outPrefix> [-L logFile]
Parameters
Required arguments: -i/--in [inputBAMFile] : Original BAM file containing readGroup info -o/--out [outPrefix] : prefix of output bam files of [outprefix].[RGID].bam Optional arguments: -L/--log [logFile] : log file name. default is listFile.log -v/--verbose : turn on verbose mode
