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== stats ==
== stats ==
The <code>stats option on the bam executable generates the specified statistics on a SAM/BAM file.
The <code>stats</code> option on the bam executable generates the specified statistics on a SAM/BAM file.
=== Parameters ===
=== Parameters ===
<pre>
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)
--baseQC : Write per base statistics to the specified file.
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 region list chr<tab>start_pos<tab>end<pos>.
Positions are 0 based and the end_pos is not included in the region.
Uses bamIndex.
--noeof : Do not expect an EOF block on a bam file.
--params : Print the parameter settings
</pre>
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.
=== Types of Statistics ===
==== Basic ====
Prints summary statistics for the file:
*TotalReads - # of reads that are in the file
*MappedReads - # of reads marked mapped in the flag
*PairedReads - # of reads marked paired in the flag
*ProperPair - # of reads marked paired AND proper paired in the flag
*DuplicateReads - # of reads marked duplicate in the flag
*QCFailureReads - # of reads marked QC failure in the flag
*MappingRate(%) - # of reads marked mapped in the flag / TotalReads
*PairedReads(%) - # of reads marked paired in the flag / TotalReads
*ProperPair(%) - # of reads marked paired AND proper paired in the flag / TotalReads
*DupRate(%) - # of reads marked duplicate in the flag / TotalReads
*QCFailRate(%) - # of reads marked QC failure in the flag / TotalReads
*TotalBases - # of bases in all reads
*BasesInMappedReads - # of bases in reads marked mapped in the flag
==== Qual/Phred ====
Prints a count of the number of times each quality value appears in the file.
*<code>phred</code> Displays Quality as phred integers [0-93]
*<code>qual</code> Displays Quality as non-phred integers (phred + 33) [33-126]
==== BaseQC ====
==== BaseQC ====
'''This capability is coming soon, so these notes may be updated prior to it being completed...'''
'''This capability is coming soon, so these notes may be updated prior to it being completed...'''
