Difference between revisions of "BamUtil: splitBam"
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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 17:44, 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