Revision as of 14:47, 7 October 2011

Overview of the `stats` function of `bamUtil`

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

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 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.
		--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

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

The optional parameters are also used for all types of statistics.

Usage:

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

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.

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.

Percentages
Straight Counts

Percentage-Based Output Format

Order/Descriptions:

Field	Description	Excludes Duplicates, QC Failures	Excludes Unmapped	Excludes MapQual = 255	Excludes Below Min MapQual
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
Q20Bases	# of bases at this position with a base quality (from the read) of Q20 or higher	X	X		X
Q20BasesPct(%)	Q20Bases / Depth	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 in version 1.0.

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

Field	Description	Excludes Duplicates, QC Failures	Excludes Unmapped	Excludes MapQual = 255	Excludes Below Min MapQual
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
Q20Bases	# of bases at this position with a base quality (from the read) of Q20 or higher	X	X		X

Difference between revisions of "BamUtil: stats"

Revision as of 14:47, 7 October 2011

Contents

Overview of the `stats` function of `bamUtil`

Parameters

Types of Statistics

Basic

Qual/Phred

BaseQC

BaseQC Output

Percentage-Based Output Format

Sample Output

Count-Based Output Format

Navigation menu

Page actions

Page actions

Personal tools

quick links

teaching

Navigation

Search

Tools

@@ Line 1: / Line 1: @@
-[[Category:BamUtil|stats]]
+<br>
-[[Category:BAM Software]]
-[[Category:Software]]
-= Overview of the <code>stats</code> function of <code>bamUtil</code> =
+= Overview of the <code>stats</code> function of <code>bamUtil</code>  =
-The <code>stats</code> option on the [[bamUtil]] executable generates the specified statistics on a SAM/BAM file.
-= Parameters =
+The <code>stats</code> option on the [[BamUtil]] executable generates the specified statistics on a SAM/BAM file.
-<pre>
-	Required Parameters:
+= Parameters  =
-		--in : the SAM/BAM file to calculate stats for
+<pre>	Required Parameters:
+		--in&nbsp;: the SAM/BAM file to calculate stats for
 	Types of Statistics that can be generated:
-		--basic       : Turn on basic statistic generation
+		--basic      &nbsp;: Turn on basic statistic generation
-		--qual        : Generate a count for each quality (displayed as non-phred quality)
+		--qual       &nbsp;: Generate a count for each quality (displayed as non-phred quality)
-		--phred       : Generate a count for each quality (displayed as phred quality)
+		--phred      &nbsp;: Generate a count for each quality (displayed as phred quality)
-		--baseQC      : Write per base statistics to the specified file.
+		--baseQC     &nbsp;: Write per base statistics to the specified file.
 	Optional Parameters:
-		--maxNumReads : Maximum number of reads to process
+		--maxNumReads&nbsp;: Maximum number of reads to process
 		                Defaults to -1 to indicate all reads.
-		--unmapped    : Only process unmapped reads (requires a bamIndex file)
+		--unmapped   &nbsp;: Only process unmapped reads (requires a bamIndex file)
-		--bamIndex    : The path/name of the bam index file
+		--bamIndex   &nbsp;: 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>.
+		--regionList &nbsp;: File containing the region list chr&lt;tab&gt;start_pos&lt;tab&gt;end&lt;pos&gt;.
 		                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.
+		--minMapQual &nbsp;: The minimum mapping quality for filtering reads in the baseQC stats.
-		--dbsnp       : The dbSnp file of positions to exclude from baseQC analysis.
+		--dbsnp      &nbsp;: The dbSnp file of positions to exclude from baseQC analysis.
-		--noeof       : Do not expect an EOF block on a bam file.
+		--noeof      &nbsp;: Do not expect an EOF block on a bam file.
-		--params      : Print the parameter settings
+		--params     &nbsp;: Print the parameter settings
 </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.
 Usage:
-<pre>
+<pre>	./bam stats --in &lt;inputFile&gt; [--basic] [--qual] [--phred] [--baseQC &lt;outputFileName&gt;] [--maxNumReads &lt;maxNum&gt;] [--unmapped] [--bamIndex &lt;bamIndexFile&gt;] [--regionList &lt;regFileName&gt;] [--minMapQual &lt;minMapQ&gt;] [--dbsnp &lt;dbsnpFile&gt;] [--noeof] [--params]
-	./bam stats --in <inputFile> [--basic] [--qual] [--phred] [--baseQC <outputFileName>] [--maxNumReads <maxNum>] [--unmapped] [--bamIndex <bamIndexFile>] [--regionList <regFileName>] [--minMapQual <minMapQ>] [--dbsnp <dbsnpFile>] [--noeof] [--params]
+</pre>
-</pre>
+<br>
+= Types of Statistics  =
+== Basic  ==
-= Types of Statistics =
+Prints summary statistics for the file:
-== Basic ==
+*TotalReads - # of reads that are in the file
-Prints summary statistics for the file:
+*MappedReads - # of reads marked mapped in the flag
-*TotalReads - # of reads that are in the file
+*PairedReads - # of reads marked paired in the flag
-*MappedReads - # of reads marked mapped in the flag
+*ProperPair - # of reads marked paired AND proper paired in the flag
-*PairedReads - # of reads marked paired in the flag
+*DuplicateReads - # of reads marked duplicate in the flag
-*ProperPair - # of reads marked paired AND proper paired in the flag
+*QCFailureReads - # of reads marked QC failure in the flag
-*DuplicateReads - # of reads marked duplicate in the flag
+*MappingRate(%) - # of reads marked mapped in the flag / TotalReads
-*QCFailureReads - # of reads marked QC failure in the flag
+*PairedReads(%) - # of reads marked paired in the flag / TotalReads
-*MappingRate(%) - # of reads marked mapped in the flag / TotalReads
+*ProperPair(%) - # of reads marked paired AND proper paired in the flag / TotalReads
-*PairedReads(%) - # of reads marked paired in the flag / TotalReads
+*DupRate(%) - # of reads marked duplicate in the flag / TotalReads
-*ProperPair(%) - # of reads marked paired AND proper paired in the flag / TotalReads
+*QCFailRate(%) - # of reads marked QC failure in the flag / TotalReads
-*DupRate(%) - # of reads marked duplicate in the flag / TotalReads
+*TotalBases - # of bases in all reads
-*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 ==
+== 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]
+Prints a count of the number of times each quality value appears in the file.
-== BaseQC ==
+*<code>phred</code> Displays Quality as phred integers [0-93]
+*<code>qual</code> Displays Quality as non-phred integers (phred + 33) [33-126]
-The <code>baseQC</code> option generates the following statistics:
+<br>
-For each position, the following counts are incremented if:
+== BaseQC  ==
-# a read spans the reference position (starts before or at this reference position and ends at or after this position)
-# regardless of duplicate/qc failure/unmapped/mapping quality
-# if CIGAR for this position is M/X/=/D/N (any cigar other than clip or insert)
-*TotalReads - # of reads that span this position.
-*Dups - # of reads marked duplicate in the flag
-*QCFail - # of reads marked QC failure in the flag
-No further stats are incremented if the read is a duplicate, QC failure, or unmapped.
+The <code>baseQC</code> option generates the following statistics:
-Additional counts incremented ONLY for mapped, non-duplicate, non-QC failure reads:
+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.
-*Mapped - # of reads marked mapped in the flag
-*Paired - # of reads marked paired in the flag
-*ProperPaired - # of reads marked paired AND proper paired in the flag
-*ZeroMapQual - # of reads that have a Mapping Quality of 0
-*MapQual<10 - # of reads that have a Mapping Quality < 10
-*MapQual255 - # of reads that have a Mapping Quality = 255
-*PassMapQual - # of reads that have a Mapping Quality >= a minimum Mapping Quality (version 1.0, this includes mapping quality 255 reads).
-Additional values ONLY for mapped, mapping quality != 255, non-duplicate, non-QC failure reads:
+Currently there is no special logic to exclude positions/reads where the reference base is 'N' or the read base is 'N'.
-*AverageMapQuality - average calculated by summing all mapping qualities that are included (as defined above) and dividing by the number of mapping qualities added.
-*AverageMapQualCount - # of mapping qualities used to calculate AverageMapQuality.
-Additional values ONLY incremented for mapped, mapping quality >= min mapping quality, non-duplicate, non-QC failure reads (version 1.0, this includes mapping quality 255 reads):
+<br>
-*Depth - # of reads.
-*Q20Bases - # of bases at this position with a base quality (from the read) of Q20 or higher.
-Currently there is no special logic to exclude positions where the refernce is 'N'.
+=== BaseQC Output  ===
-Currently there is no special logic to exclude reads from the counts when the base is 'N'.
+There are two output options for BaseQC.
+#Percentages
+#Straight Counts
-=== BaseQC Output ===
+==== Percentage-Based Output Format  ====
-There are two output options for BaseQC.
-# Percentages
-# Straight Counts
-==== Percentage-Based Output Format ====
+Order/Descriptions:
-Order (with calculations based on the values described above):
-*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 - Depth
-*Q20Bases - Q20Bases
-*Q20BasesPct(%) - Q20Bases / Depth
-*TotalReads - TotalReads
-*MappedBases - Mapped
-*MappingRate(%) - Mapped / TotalReads
-*MapRate_MQPass(%) - PassMapQual / TotalReads
-*ZeroMapQual(%) - ZeroMapQual / TotalReads
-*MapQual<10(%) - MapQual<10 / TotalReads
-*PairedReads(%) - Paired / TotalReads
-*ProperPaired(%) - ProperPaired / TotalReads
-*DupRate(%) - Dups / TotalReads
-*QCFailRate(%) - QCFail / TotalReads
-*AverageMapQuality - AverageMapQuality
-*AverageMapQualCount - AverageMapQualCount
-This output does not include a MapQual255 count in version 1.0.
+{|border=1
+! Field !! Description !!style="width: 80px"| Excludes Duplicates, QC Failures !!style="width: 80px"| Excludes Unmapped !!style="width: 80px"|  Excludes MapQual = 255 !!style="width: 80px"| Excludes Below Min MapQual
+|-
+| 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 || align="center"|X || align="center"|X || || align="center"|X
+|-
+| Q20Bases || # of bases at this position with a base quality (from the read) of Q20 or higher || align="center"|X || align="center"|X || || align="center"|X
+|-
+| Q20BasesPct(%) || Q20Bases / Depth || align="center"|X || align="center"|X || || align="center"|X
+|-
+| TotalReads || # of reads that span this position || || || ||
+|-
+| MappedBases || # of reads marked mapped in the flag || align="center"|X || align="center"|X || ||
+|-
+| MappingRate(%) || MappedBases / TotalReads || align="center"|X || align="center"|X || ||
+|-
+| MapRate_MQPass(%) || # of reads that have a Mapping Quality &gt;= a minimum Mapping Quality / TotalReads || align="center"|X || align="center"|X || ||
+|-
+| ZeroMapQual(%) || # of reads that have a Mapping Quality of 0 / TotalReads || align="center"|X || align="center"|X || ||
+|-
+| MapQual&lt;10(%) || # of reads that have a Mapping Quality &lt; 10 / TotalReads || align="center"|X || align="center"|X || ||
+|-
+| PairedReads(%) || # of reads marked paired in the flag / TotalReads || align="center"|X || align="center"|X || ||
+|-
+| ProperPaired(%) || # of reads marked paired AND proper paired in the flag / TotalReads || align="center"|X || align="center"|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 || align="center"|X || align="center"|X || align="center"|X ||
+|-
+| AverageMapQualCount || # of mapping qualities in AverageMapQuality || align="center"|X || align="center"|X || align="center"|X ||
+|-
+|}
+This output does not include a MapQual255 count in version 1.0.
-==== Count-Based Output Format ====
+===== Sample Output  =====
-Order (of values described above):
+<pre>chrom	chromStart	chromEnd	Depth	Q20Bases	Q20BasesPct(%)	TotalReads	MappedBases	MappingRate(%)	MapRate_MQPass(%)	ZeroMapQual(%)	MapQual&lt;10(%)	PairedReads(%)	ProperPaired(%)	DupRate(%)	QCFailRate(%)	AverageMapQuality	AverageMapQualCount
-*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
-*Dups
-*QCFail
-*Mapped
-*Paired
-*ProperPaired
-*ZeroMapQual
-*MapQual<10
-*MapQual255
-*PassMapQual
-*AverageMapQuality
-*AverageMapQualCount
-*Depth
-*Q20Bases
-=== Sample Output ===
-<pre>
-chrom	chromStart	chromEnd	Depth	Q20Bases	Q20BasesPct(%)	TotalReads	MappedBases	MappingRate(%)	MapRate_MQPass(%)	ZeroMapQual(%)	MapQual<10(%)	PairedReads(%)	ProperPaired(%)	DupRate(%)	QCFailRate(%)	AverageMapQuality	AverageMapQualCount
 	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
 	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
@@ Line 168: / Line 144: @@
 	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
 	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
 </pre>
+==== Count-Based Output Format  ====
+{|border=1
+! Field !! Description !!style="width: 80px"| Excludes Duplicates, QC Failures !!style="width: 80px"| Excludes Unmapped !!style="width: 80px"|  Excludes MapQual = 255 !!style="width: 80px"| Excludes Below Min MapQual
+|-
+| 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 || align="center"|X || align="center"|X || ||
+|-
+| Paired || # of reads marked paired in the flag || align="center"|X || align="center"|X || ||
+|-
+| ProperPaired || # of reads marked paired AND proper paired in the flag || align="center"|X || align="center"|X || ||
+|-
+| ZeroMapQual || # of reads that have a Mapping Quality of 0 || align="center"|X || align="center"|X || ||
+|-
+| MapQual&lt;10(%) || # of reads that have a Mapping Quality &lt; 10 || align="center"|X || align="center"|X || ||
+|-
+| MapQual255 || # of reads that have a Mapping Quality = 255 || align="center"|X || align="center"|X || ||
+|-
+| PassMapQual || # of reads that have a Mapping Quality &gt;= a minimum Mapping Quality || align="center"|X || align="center"|X || ||
+|-
+| AverageMapQuality || sum of included mapping qualities / AverageMapQualCount || align="center"|X || align="center"|X || align="center"|X ||
+|-
+| AverageMapQualCount || # of mapping qualities in AverageMapQuality || align="center"|X || align="center"|X || align="center"|X ||
+|-
+| Depth || # of reads that are mapped with acceptable Mapping Quality, and are not duplicates or QC failures || align="center"|X || align="center"|X || || align="center"|X
+|-
+| Q20Bases || # of bases at this position with a base quality (from the read) of Q20 or higher || align="center"|X || align="center"|X || || align="center"|X
+|-
+|}
+[[Category:BamUtil|stats]] [[Category:BAM_Software]] [[Category:Software]]

Difference between revisions of "BamUtil: stats"

Revision as of 14:47, 7 October 2011

Overview of the stats function of bamUtil

Parameters

Types of Statistics

Basic

Qual/Phred

BaseQC

BaseQC Output

Percentage-Based Output Format

Sample Output

Count-Based Output Format

Navigation menu

Search

Overview of the `stats` function of `bamUtil`