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The <code>stats</code> option on the [[BamUtil]] executable generates the specified statistics on a SAM/BAM file.
The <code>stats</code> option on the [[BamUtil]] executable generates the specified statistics on a SAM/BAM file.
= Usage =
<pre>
./bam stats --in <inputFile> [--basic] [--qual] [--phred] [--baseQC <outputFileName>] [--maxNumReads <maxNum>][--unmapped] [--bamIndex <bamIndexFile>] [--regionList <regFileName>] [--minMapQual <minMapQ>] [--dbsnp <dbsnpFile>] [--sumStats] [--noeof] [--params]
</pre>
= Parameters =
= Parameters =
<pre> Required Parameters:
<pre>
--in : the SAM/BAM file to calculate stats for
Required Parameters:
--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)
--baseQC : Write per base statistics to the specified file.
--baseQC : Write per base statistics to the specified file.
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 region list 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.
--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.
--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 Base QC Only Parameters:
--sumStats : Alternate summary output.
</pre>
</pre>
For all types of statistics, the bam file used is specified by <code>--in</code>.
For all types of statistics, the bam file used is specified by <code>--in</code>.
The optional parameters are also used for all types of statistics.
The optional parameters are also used for all types of statistics.
= Types of Statistics =
= Types of Statistics =
