BamUtil: stats

Overview of the stats function of bamUtil

The stats option on the BamUtil executable generates the specified statistics on a SAM/BAM file.

Usage

./bam stats --in <inputFile> [--basic] [--qual] [--phred] [--baseQC <outputFileName>] [--maxNumReads <maxNum>][--unmapped] [--bamIndex <bamIndexFile>] [--regionList <regFileName>] [--minMapQual <minMapQ>] [--dbsnp <dbsnpFile>] [--sumStats] [--noeof] [--params]

Parameters

	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 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.
		                Uses bamIndex.
		--minMapQual  : The minimum mapping quality for filtering reads in the baseQC stats.
		--dbsnp       : The dbSnp file of positions to exclude from baseQC analysis.
		--noeof       : Do not expect an EOF block on a bam file.
		--params      : Print the parameter settings
	Optional Base QC Only Parameters:
		--sumStats    : Alternate summary output.

For all types of statistics, the bam file used is specified by --in.

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.

• phred Displays Quality as phred integers [0-93]
• qual Displays Quality as non-phred integers (phred + 33) [33-126]

BaseQC

The baseQC option generates the following statistics:

A read spans a position if the read starts at or before the position, ends at or after the position and the position is not a clip. CIGAR operations allowed for the position are M/X/=/D/N. If the CIGAR is '*', only numbers for the specified reference position are incremented.

Currently there is no special logic to exclude positions/reads where the reference base is 'N' or the read base is 'N'.

BaseQC Output

There are two output options for BaseQC.

1. Percentage-Based Output Format
2. Count-Based Output Format

Percentage-Based Output Format

Order/Descriptions:

Field	Description	Excludes Duplicates, QC Failures	Excludes Unmapped	Excludes MapQual = 255	Excludes Below Min MapQual	Excludes CIGAR Deletions, Skips
chrom	Chromosome/reference name string from the SAM/BAM
chromStart	0-based start position
chromEnd	0-based end position (always 1 greater than start and not included in this region)
Depth	# of reads that are mapped with acceptable Mapping Quality, and are not duplicates or QC failures	X	X	X	X	X
Q20Bases	# of bases at this position with a base quality (from the read) of Q20 or higher	X	X	X	X	X
Q20BasesPct(%)	Q20Bases / Depth	X	X	X	X	X
TotalReads	# of reads that span this position
MappedBases	# of reads marked mapped in the flag	X	X
MappingRate(%)	MappedBases / TotalReads	X	X
MapRate_MQPass(%)	# of reads that have a Mapping Quality >= a minimum Mapping Quality / TotalReads	X	X
ZeroMapQual(%)	# of reads that have a Mapping Quality of 0 / TotalReads	X	X
MapQual<10(%)	# of reads that have a Mapping Quality < 10 / TotalReads	X	X
PairedReads(%)	# of reads marked paired in the flag / TotalReads	X	X
ProperPaired(%)	# of reads marked paired AND proper paired in the flag / TotalReads	X	X
DupRate(%)	# of reads marked duplicate in the flag / TotalReads
QCFailRate(%)	# of reads marked QC failure in the flag / TotalReads
AverageMapQuality	sum of included mapping qualities / AverageMapQualCount	X	X	X
AverageMapQualCount	# of mapping qualities in AverageMapQuality	X	X	X

This output does not include a MapQual255 count.

Sample Output

chrom	chromStart	chromEnd	Depth	Q20Bases	Q20BasesPct(%)	TotalReads	MappedBases	MappingRate(%)	MapRate_MQPass(%)	ZeroMapQual(%)	MapQual<10(%)	PairedReads(%)	ProperPaired(%)	DupRate(%)	QCFailRate(%)	AverageMapQuality	AverageMapQualCount
1	100	101	2	2	100.000	3	3	100.000	66.667	33.333	66.667	100.000	0.000	0.000	0.000	11.000	3
1	101	102	2	0	0.000	3	3	100.000	66.667	33.333	66.667	100.000	0.000	0.000	0.000	11.000	3
1	102	103	0	0	0.000	3	3	100.000	66.667	33.333	66.667	100.000	0.000	0.000	0.000	0.000	0
1	103	104	0	0	0.000	3	3	100.000	66.667	33.333	66.667	100.000	0.000	0.000	0.000	0.000	0
1	104	105	2	0	0.000	3	3	100.000	66.667	33.333	66.667	100.000	0.000	0.000	0.000	11.000	3
1	105	106	2	2	100.000	3	3	100.000	66.667	33.333	66.667	100.000	0.000	0.000	0.000	11.000	3
1	110	111	0	0	0.000	3	3	100.000	66.667	33.333	66.667	100.000	0.000	0.000	0.000	0.000	0
1	111	112	2	2	100.000	3	3	100.000	66.667	33.333	66.667	100.000	0.000	0.000	0.000	11.000	3
1	112	113	2	2	100.000	3	3	100.000	66.667	33.333	66.667	100.000	0.000	0.000	0.000	11.000	3
1	10012	10013	14	0	0.000	42	33	78.571	52.381	26.190	52.381	85.714	35.714	14.286	14.286	11.000	21
1	10013	10014	14	10	71.429	39	30	76.923	51.282	25.641	51.282	84.615	38.462	15.385	15.385	11.000	21
1	10023	10024	0	0	0.000	39	30	76.923	51.282	25.641	51.282	84.615	38.462	15.385	15.385	0.000	0
1	10024	10025	14	12	85.714	39	30	76.923	51.282	25.641	51.282	84.615	38.462	15.385	15.385	11.000	21

Count-Based Output Format

Order/Descriptions:

Field	Description	Excludes Duplicates, QC Failures	Excludes Unmapped	Excludes MapQual = 255	Excludes Below Min MapQual	Excludes CIGAR Deletions, Skips
chrom	Chromosome/reference name string from the SAM/BAM
chromStart	0-based start position
chromEnd	0-based end position (always 1 greater than start and not included in this region)
TotalReads	# of reads that span this position
Dups	# of reads marked duplicate in the flag
QCFail	# of reads marked QC failure in the flag
Mapped	# of reads marked mapped in the flag	X	X
Paired	# of reads marked paired in the flag	X	X
ProperPaired	# of reads marked paired AND proper paired in the flag	X	X
ZeroMapQual	# of reads that have a Mapping Quality of 0	X	X
MapQual<10(%)	# of reads that have a Mapping Quality < 10	X	X
MapQual255	# of reads that have a Mapping Quality = 255	X	X
PassMapQual	# of reads that have a Mapping Quality >= a minimum Mapping Quality	X	X
AverageMapQuality	sum of included mapping qualities / AverageMapQualCount	X	X	X
AverageMapQualCount	# of mapping qualities in AverageMapQuality	X	X	X
Depth	# of reads that are mapped with acceptable Mapping Quality, and are not duplicates or QC failures	X	X	X	X	X
Q20Bases	# of bases at this position with a base quality (from the read) of Q20 or higher	X	X	X	X	X