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