BamUtil: readIndexedBam
From Genome Analysis Wiki
Jump to navigationJump to search
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