BamUtil: splitBam: Difference between revisions
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Add SplitBam to Bamutil |
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= | = Overview of the <code>splitBam</code> function of <code>bamUtil</code> = | ||
The <code>splitBam</code> 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 | # 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. | # 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 | # Copy each of the original file's BAM record to one of the output file where the ReadGroup ID matches | ||
= Usage = | |||
<pre> | <pre> | ||
Usage : splitBAM [-v] -i <inputBAMFile> -o <outPrefix> [-L logFile] | Usage : ./bam splitBAM [-v] -i <inputBAMFile> -o <outPrefix> [-L logFile] | ||
</pre> | |||
= Parameters = | |||
Required arguments: | Required arguments: | ||
-i/--in [inputBAMFile] : Original BAM file containing readGroup info | -i/--in [inputBAMFile] : Original BAM file containing readGroup info | ||
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</pre> | </pre> | ||
[[Category:BamUtil|splitChromosome]] | |||
[[Category:BAM Software]] | |||
[[Category:Software]] | [[Category:Software]] | ||
Revision as of 21:44, 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
