BamUtil: readIndexedBam

Overview of the readIndexedBam function of bamUtil

The readIndexedBam option on the bamUtil executable reads an indexed BAM file reference id by reference id, from -1 to the max reference id and writes it out as a SAM/BAM file.

For more flexibility of writing specific regions, see BamUtil: writeRegion.

Parameters

	Required Parameters:
		inputFilename      - path/name of the input BAM file
		outputFile.sam/bam - path/name of the output file
		bamIndexFile       - path/name of the BAM index file

Usage

./bam readIndexedBam <inputFilename> <outputFile.sam/bam> <bamIndexFile>

Return Value

• 0