BamUtil: readReference

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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.


	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


./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.

Example Output