Difference between revisions of "BamUtil: splitBam"
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Usage : splitBAM [-v] [-i inputBAMFile] [-o outPrefix] [-L logFile] | Usage : splitBAM [-v] [-i inputBAMFile] [-o outPrefix] [-L logFile] | ||
Required arguments: | Required arguments: | ||
| − | -i inputBAMFile : Original BAM file containing readGroup info | + | -i/--in [inputBAMFile] : Original BAM file containing readGroup info |
| − | -o | + | -o/--out [outPrefix] : prefix of output bam files of [outprefix].[RGID].bam |
Optional arguments: | Optional arguments: | ||
| − | -L logFile : log file name. default is listFile.log | + | -L/--log [logFile] : log file name. default is listFile.log |
| − | -v : turn on verbose mode | + | -v/--verbose : turn on verbose mode |
</pre> | </pre> | ||
Revision as of 18:44, 1 November 2010
SplitBam
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 : splitBAM [-v] [-i inputBAMFile] [-o outPrefix] [-L logFile]
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
