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BamUtil: stats (view source)

Revision as of 11:57, 7 October 2011

38 bytes added ,  11:57, 7 October 2011
Update BaseQC outputs
Line 72: Line 72:  
# a read spans the reference position (starts before or at this reference position and ends at or after this position)
 
# 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
 
# regardless of duplicate/qc failure/unmapped/mapping quality
−
# regardless of the CIGAR for this position (other than clips at the beginning/end which are not counted, but deletions and skips are counted)
+
# if CIGAR for this position is M/X/=/D/N (any cigar other than clip or insert)
 
*TotalReads - # of reads that span this position.  
 
*TotalReads - # of reads that span this position.  
−
*DupRate(%) - # of reads marked duplicate in the flag / TotalReads
+
*Dups - # of reads marked duplicate in the flag
−
*QCFailRate(%) - # of reads marked QC failure in the flag / TotalReads
+
*QCFail - # of reads marked QC failure in the flag
−
*PairedReads(%) - # of reads marked paired in the flag / TotalReads
  −
*ProperPaired(%) - # of reads marked paired AND proper paired in the flag / TotalReads
  −
*MappedBases - # of reads marked mapped in the flag
  −
*MappingRate(%) - # of reads marked mapped in the flag / TotalReads
  −
*ZeroMapQual(%) - # of reads marked mapped in the flag AND have a Mapping Quality of 0 / TotalReads
  −
*MapQual<10(%) - # of reads marked mapped in the flag AND have a Mapping Quality < 10 / TotalReads
  −
*MapRate_MQpass(%) - # of reads marked mapped in the flag AND have a Mapping Quality >= a minimum Mapping Quality / TotalReads
      +
No further stats are incremented if the read is a duplicate, QC failure, or unmapped.
   −
For each position, the following counts exclude:
+
Additional counts incremented ONLY for mapped, non-duplicate, non-QC failure reads:
−
# unmapped reads
+
*Mapped - # of reads marked mapped in the flag
−
# duplicates
+
*Paired - # of reads marked paired in the flag
−
# failed QC
+
*ProperPaired - # of reads marked paired AND proper paired in the flag
−
# deletions/skips (only CIGAR M/X/= are included)
+
*ZeroMapQual - # of reads that have a Mapping Quality of 0
−
# MapQ below the min
+
*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:
 +
*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):
 
*Depth - # of reads.   
 
*Depth - # of reads.   
 
*Q20Bases - # of bases at this position with a base quality (from the read) of Q20 or higher.
 
*Q20Bases - # of bases at this position with a base quality (from the read) of Q20 or higher.
−
*Q20BasesPct(%) - Q20Bases / Depth
+
 
 +
Currently there is no special logic to exclude positions where the refernce is 'N'.
 +
 
 +
Currently there is no special logic to exclude reads from the counts when the base is 'N'.
      −
For each position, the following counts exclude:
+
=== BaseQC Output ===
−
# unmapped reads
+
There are two output options for BaseQC.
−
# duplicates
+
# Percentages
−
# failed QC
+
# Straight Counts
−
# deletions/skips (only CIGAR M/X/= are included)
  −
# MapQ of 255
  −
*AverageMapQuality - average calculated by summing all mapping qualities that are not excluded (as defined above) and dividing by the number of mapping qualities added.
  −
*AverageMapQualCount - # of mapping qualities used to calculate AverageMapQuality.
     −
Currently there is no special logic to exclude positions where the refernce is 'N'.
+
==== Percentage-Based Output Format ====
 +
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
   −
Currently there is no special logic to exclude reads from the counts when the base is 'N'.
+
This output does not include a MapQual255 count in version 1.0.
      −
=== Output Format ===
+
==== Count-Based Output Format ====
−
Order:
+
Order (of values described above):
 
*chrom - Chromosome/reference name string from the SAM/BAM
 
*chrom - Chromosome/reference name string from the SAM/BAM
 
*chromStart - 0-based start position  
 
*chromStart - 0-based start position  
 
*chromEnd  - 0-based end position (always 1 greater than start and not included in this region)
 
*chromEnd  - 0-based end position (always 1 greater than start and not included in this region)
−
*Depth - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ below the min
+
*TotalReads
−
*Q20Bases - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ below the min
+
*Dups
−
*Q20BasesPct(%) - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ below the min
+
*QCFail
−
*TotalReads - only excludes clips
+
*Mapped
−
*MappedBases - only excludes clips
+
*Paired
−
*MappingRate(%) - only excludes clips
+
*ProperPaired
−
*MapRate_MQPass(%) - only excludes clips
+
*ZeroMapQual
−
*ZeroMapQual(%) - only excludes clips
+
*MapQual<10
−
*MapQual<10(%) - only excludes clips
+
*MapQual255
−
*PairedReads(%) - only excludes clips
+
*PassMapQual
−
*ProperPaired(%) - only excludes clips
+
*AverageMapQuality
−
*DupRate(%) - only excludes clips
+
*AverageMapQualCount
−
*QCFailRate(%) - only excludes clips
+
*Depth
−
*AverageMapQuality - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ 255
+
*Q20Bases
−
*AverageMapQualCount - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ 255
+
 
    
=== Sample Output ===
 
=== Sample Output ===
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/3910"

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