From Genome Analysis Wiki
= Parameters =
Required Parameters: --in : the SAM/BAM file to calculate stats for Types of Statistics that can be generated: --basic : Turn on basic statistic generation --qual : Generate a count for each quality (displayed as non-phred quality) --phred : Generate a count for each quality (displayed as phred quality) --pBaseQC : Write per base statistics as Percentages to the specified file. pBaseQC & cBaseQC cannot both be specified. --cBaseQC : Write per base statistics as Counts to the specified file. pBaseQC & cBaseQC cannot both be specified. Optional Parameters: --maxNumReads : Maximum number of reads to process Defaults to -1 to indicate all reads. --unmapped : Only process unmapped reads (requires a bamIndex file) --bamIndex : The path/name of the bam index file (if required and not specified, uses the --in value + ".bai") --regionList : File containing the regions to be processed chr<tab>start_pos<tab>end_pos. Positions are 0 based and the end_pos is not included in the region. Uses bamIndex. --excludeFlags : Skip any records with any of the specified flags set (specify an integer representation of the flags) --requiredFlags : Only process records with all of the specified flags set (specify an integer representation of the flags) --noeof : Do not expect an EOF block on a bam file. --params : Print the parameter settings. Optional phred/qual Only Parameters: --withinRegion : Only count qualities if they fall within regions specified. Only applicable if regionList is also specified. Optional BaseQC Only Parameters: --baseSum : Print an overall summary of the baseQC for the file to stderr. --bufferSize : Size of the pileup buffer for calculating the BaseQC parameters. Default: 1024 --minMapQual : The minimum mapping quality for filtering reads in the baseQC stats. --dbsnp : The dbSnp file of positions to exclude from baseQC analysis.