BamUtil: splitBam: Difference between revisions
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# Copy each of the original file's BAM record to one of the output file where the ReadGroup ID matches | # Copy each of the original file's BAM record to one of the output file where the ReadGroup ID matches | ||
<pre> | <pre> | ||
Usage : splitBAM [-v] | Usage : splitBAM [-v] -i <inputBAMFile> -o <outPrefix> [-L logFile] | ||
Required arguments: | Required arguments: | ||
-i/--in [inputBAMFile] : Original BAM file containing readGroup info | -i/--in [inputBAMFile] : Original BAM file containing readGroup info | ||
Revision as of 22:47, 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
