Changes

== SplitBam ==

= Overview of the <code>splitBam</code> function of <code>bamUtil</code> =

Split a BAM file into multiple BAM files based on ReadGroup according to the following details.

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

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  Usage : splitBAM [-v] -i <inputBAMFile> -o <outPrefix> [-L logFile]

  Usage : ./bam 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

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[[Category:Software]]

[[Category:Software]]