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BamUtil

2,340 bytes added, 10:17, 30 August 2011
stats
== stats ==
The <code>stats </code> option on the bam executable generates the specified statistics on a SAM/BAM file.
=== 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]
 
=== Notes ===
==== BaseQC ====
'''This capability is coming soon, so these notes may be updated prior to it being completed...'''

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