BamUtil: readReference
From Genome Analysis Wiki
Jump to navigationJump to search
Overview of the readReference
function of bamUtil
The readReference
option on the bamUtil executable prints the specified region of the reference sequence in an easy to read format.
Parameters
Required Parameters: --refFile : the reference --refName : the SAM/BAM reference Name to read --start : inclusive 0-based start position --params : print the parameter settings Required Length Parameter (one but not both needs to be specified): --end : exclusive 0-based end position --numBases : number of bases from start to display
Usage
./bam readReference --refFile <referenceFilename> --refName <reference Name> --start <0 based start> --end <0 based end>|--numBases <number of bases> [--params]
Return Value
- 0: the reference file was successfully read.
- non-0: the reference file was not successfully read.