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= Parameters =
= Parameters =
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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. (use - for stdout)
pBaseQC & cBaseQC cannot both be specified.
--cBaseQC : Write per base statistics as Counts to the specified file. (use - for stdout)
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.
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