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= Usage =
= Usage =
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./bam stats --in <inputFile> [--basic] [--qual] [--phred] [--pBaseQC <outputFileName>] [--cBaseQC <outputFileName>] [--maxNumReads <maxNum>][--unmapped] [--bamIndex <bamIndexFile>] [--regionList <regFileName>] [--requiredFlags <integerRequiredFlags>] [--excludeFlags <integerExcludeFlags>] [--noeof] [--params] [--withinRegion] [--baseSum] [--bufferSize <buffSize>] [--minMapQual <minMapQ>] [--dbsnp <dbsnpFile>]
./bam stats --in <inputFile> [--basic] [--qual] [--phred] [--pBaseQC <outputFileName>] [--cBaseQC <outputFileName>] [--maxNumReads <maxNum>][--unmapped] [--bamIndex <bamIndexFile>] [--regionList <regFileName>] [--requiredFlags <integerRequiredFlags>] [--excludeFlags <integerExcludeFlags>] [--noeof] [--params] [--withinRegion] [--baseSum] [--bufferSize <buffSize>] [--minMapQual <minMapQ>] [--dbsnp <dbsnpFile>]
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--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.
--dbsnp : The dbSnp file of positions to exclude from baseQC analysis.
--dbsnp : The dbSnp file of positions to exclude from baseQC analysis.
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{{PhoneHomeParamDesc}}
== Required Parameters ==
{{inBAMInputFile}}
{{inBAMInputFile}}
== Optional Parameters ==
=== Maximum number of reads to process(<code>--maxNumReads</code>) ===
Use <code>--maxNumReads</code> followed by a number to indicate the maximum number of reads to process before exiting. By default, it is set to -1 to indicate all reads should be processed.
=== Only Process Unmapped Reads (<code>--unmapped</code>) ===
Use <code>--unmapped</code> to process only unmapped reads.
This parameter requires [[#Bam Index File (--bamIndex)|<code>--bamIndex</code>]].
{{BamIndex}}
=== Only Process Certain Regions (<code>--regionList</code>) ===
Use <code>--regionList</code> followed by the filename to process only the regions specified in the file.
The positions in the file are specified one per line with the following format: <nowiki>chr<tab>start_pos<tab>end_pos.</nowiki>
Positions are 0 based and the end_pos is not included in the region.
This parameter requires [[#Bam Index File (--bamIndex)|<code>--bamIndex</code>]].
=== Exclude Flags (<code>--excludeFlags</code>) ===
Use <code>--excludeFlags</code> followed by an integer representation of the flags to only process reads with any of the specified flags set.
=== Required Flags (<code>--requiredFlags</code>) ===
Use <code>--requiredFlags</code> followed by an integer representation of the flags to only process records with all of the specified flags set.
== Types of Statistics ==
== Types of Statistics ==
To only include records that overlap a set of regions, use --regionList and specify a bed file with the regions. If a read overlaps the region, all qualities will be counted even if those bases do not fall in the region. If you only want to count qualities that fall within the region, also specify --withinRegion. Without excluding unmapped reads, it will include soft clips that overlap the region.
To only include records that overlap a set of regions, use --regionList and specify a bed file with the regions. If a read overlaps the region, all qualities will be counted even if those bases do not fall in the region. If you only want to count qualities that fall within the region, also specify --withinRegion. Without excluding unmapped reads, it will include soft clips that overlap the region.
<br>
==== Optional Phred/Qual Only Parameters ====
===== Within Region (<code>--withinRegion</code>) =====
Use <code>--withinRegion</code> with [[#Qual/Phred (--phred and --qual)|<code>--phred</code> or <code>--qual</code>]] options to only count qualities if they fall within the regions specified using [[#Only Process Certain Regions (--regionList)|<code>--regionList</code>]] (only applicable if [[#Only Process Certain Regions (--regionList)|<code>--regionList</code>]] is also specified).
=== BaseQC (<code>--pBaseQC</code> and <code>--cBaseQC</code> and <code>--baseSum</code>) ===
=== BaseQC (<code>--pBaseQC</code> and <code>--cBaseQC</code> and <code>--baseSum</code>) ===
17.670053 2.882307 2.882307 9.038380 7.603137 1.441153 3.012793 6.025586 0.000000 3.012793 0.000000 9.038380 2.841993 1.993579
17.670053 2.882307 2.882307 9.038380 7.603137 1.441153 3.012793 6.025586 0.000000 3.012793 0.000000 9.038380 2.841993 1.993579
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==== Optional BaseQC Only Parameters ====
===== Pileup Buffer Size (<code>--bufferSize</code>) =====
Use the <code>--bufferSize</code> option followed by the size of the pileup buffer to use for [[BaseQC (--pBaseQC and --cBaseQC and --baseSum)|baseQC]] stats.
===== Minimum Mapping Quality (<code>--minMapQual</code>) =====
Use the <code>--minMapQual</code> option followed by the minimum mapping quality for filtering reads in the [[BaseQC (--pBaseQC and --cBaseQC and --baseSum)|baseQC]] stats.
===== DBSNP File (<code>--dbsnp</code>) =====
Use the <code>--dbsnp</code> option followed by the name of the dbsnp file to specify the positions to exclude from [[BaseQC (--pBaseQC and --cBaseQC and --baseSum)|baseQC]] analysis.
{{PhoneHomeParameters}}
= Return Value =
0 on Success, non-0 on failure
[[Category:BamUtil|stats]] [[Category:BAM_Software]] [[Category:Software]]
[[Category:BamUtil|stats]] [[Category:BAM_Software]] [[Category:Software]]
