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BamUtil

17,218 bytes removed, 14:35, 2 September 2011
Split into mulitple pages and add missing tools
(It will be available without libStatGen in case you already have a downloaded version of libStatGen that you want to use.
=== Using github Releases ===Releases Release downloads are '''Coming Soon'''.
The bam executable has the following functions.
* [[C++ ExecutableBamUtil: bam#validate|validate|validate - Read and Validate a SAM/BAM file]]
* [[BamUtil: convert|convert - Read a SAM/BAM file and write as a SAM/BAM file (optionally converts between '=' & bases in the sequence)]]
* [[C++ ExecutableBamUtil: bam#dumpHeader|dumpHeader - Print SAM/BAM header]]* [[C++ ExecutableBamUtil: bam#splitChromosome|splitChromosome - Split BAM by Chromosome]]* [[C++ ExecutableBamUtil: bam#writeRegion|writeRegion - Write the alignments in the indexed BAM file that fall into the specified region]]* [[C++ ExecutableBamUtil: bam#dumpRefInfo|dumpRefInfo - Print SAM/BAM Reference Information]]* [[C++ ExecutableBamUtil: bam#dumpIndex|dumpIndex - Dump a BAM index file into an easy to read text version]]* [[C++ ExecutableBamUtil: bam#readIndexedBam|readIndexedBam - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file]]* [[C++ ExecutableBamUtil: bam#filter|filter - Filter reads by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high]]* [[C++ ExecutableBamUtil: bam#readReference|readReference - Print the reference string for the specified region]]* [[C++ ExecutableBamUtil: bam#diff|diff - Print the diffs between 2 bams]]* [[BamUtil: stats|stats - Print the diffs between 2 bams]]* [[BamUtil: revert|revert - Revert SAM/BAM replacing the specified fields with their previous values (if known).]]* [[BamUtil: squeeze|squeeze - reduces files size by dropping OQ fields, duplicates, specified tags, using '=' when a base matches the reference, binning quality scores.]]* [[BamUtil: findCigars|findCigars - Output just the reads that contain any of the specified CIGAR operations.]]
This executable is built using [[C++ Library: libStatGen]].
Just running ./bam will print the Usage information for the bam executable.
 
 
== validate ==
 
The <code>validate</code> option on the bam executable reads and validates a SAM/BAM file. This option is documented at: [[BamValidator]]
 
== dumpHeader ==
The <code>dumpHeader</code> option on the bam executable prints the header of the specified SAM/BAM file to cout.
 
=== Parameters ===
<pre>
Required Parameters:
filename : the sam/bam filename whose header should be printed.
</pre>
 
=== Usage ===
 
./bam dumpHeader <inputFile>
 
=== Return Value ===
* 0: the header was successfully read and printed.
* non-0: the header was not successfully read or was not printed. (Returns the SamStatus.)
 
 
=== Example Output ===
<pre>
@SQ SN:1 LN:247249719
@SQ SN:2 LN:242951149
@SQ SN:3 LN:199501827
</pre>
 
 
== splitChromosome ==
 
The <code>splitChromosome</code> option on the bam executable splits an indexed BAM file into multiple files based on the Chromosome (Reference Name).
 
The files all have the same base name, but with an _# where # corresponds with the associated reference id from the BAM file.
 
=== Parameters ===
<pre>
Required Parameters:
--in : the BAM file to be split
--out : the base filename for the SAM/BAM files to write into. Does not include the extension.
_N will be appended to the basename where N indicates the Chromosome.
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
--bamIndex : the path/name of the bam index file
(if not specified, uses the --in value + ".bai")
--bamout : write the output files in BAM format (default).
--samout : write the output files in SAM format.
--params : print the parameter settings
</pre>
 
=== Usage ===
 
./bam splitChromosome --in <inputFilename> --out <outputFileBaseName> [--bamIndex <bamIndexFile>] [--noeof] [--bamout|--samout] [--params]
 
 
=== Return Value ===
* 0: all records are successfully read and written.
* non-0: at least one record was not successfully read or written.
 
=== Example Output ===
<pre>
Reference ID -1 has 2 records
Reference ID 0 has 5 records
Reference ID 1 has 2 records
Reference ID 2 has 1 records
Reference ID 3 has 0 records
Reference ID 4 has 0 records
Reference ID 5 has 0 records
Reference ID 6 has 0 records
Reference ID 7 has 0 records
Reference ID 8 has 0 records
Reference ID 9 has 0 records
Reference ID 10 has 0 records
Reference ID 11 has 0 records
Reference ID 12 has 0 records
Reference ID 13 has 0 records
Reference ID 14 has 0 records
Reference ID 15 has 0 records
Reference ID 16 has 0 records
Reference ID 17 has 0 records
Reference ID 18 has 0 records
Reference ID 19 has 0 records
Reference ID 20 has 0 records
Reference ID 21 has 0 records
Reference ID 22 has 0 records
Number of records = 10
Returning: 0 (SUCCESS)
</pre>
 
 
== writeRegion ==
 
The <code>writeRegion</code> option on the bam executable writes the alignments in the indexed BAM file that fall into the specified region (reference id and start/end position).
 
=== Parameters ===
<pre>
Required Parameters:
--in : the BAM file to be read
--out : the SAM/BAM file to write to
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
--bamIndex : the path/name of the bam index file
(if not specified, uses the --in value + ".bai")
--refName : the BAM reference Name to read (either this or refID can be specified)
--refID : the BAM reference ID to read (defaults to -1: unmapped)
--start : inclusive 0-based start position (defaults to -1)
--end : exclusive 0-based end position (defaults to -1: meaning til the end of the reference)
--params : print the parameter settings
</pre>
 
=== Usage ===
 
./bam writeRegion --in <inputFilename> --out <outputFilename> [--bamIndex <bamIndexFile>] [--noeof] [--refName <reference Name> | --refID <reference ID>] [--start <0-based start pos>] [--end <0-based end psoition>] [--params]
=== Return Value ===
* 0: all records are successfully read and written.
* non-0: at least one record was not successfully read or written.
 
=== Example Output ===
<pre>
 
Wrote t.sam with 2 records.
</pre>
 
 
== dumpRefInfo ==
The <code>dumpRefInfo</code> option on the bam executable prints the SAM/BAM file's reference information.
 
=== Parameters ===
<pre>
Required Parameters:
--in : the SAM/BAM file to be read
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
--printRecordRefs : print the reference information for the records in the file (grouped by reference).
--params : print the parameter settings
</pre>
 
=== Usage ===
./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs] [--params]
 
=== Return Value ===
* 0: the file was processed successfully.
* non-0: the file was not processed successfully.
 
 
== dumpIndex ==
The <code>dumpIndex</code> option on the bam executable prints BAM index file in an easy to read format.
 
=== Parameters ===
<pre>
Required Parameters:
--bamIndex : the path/name of the bam index file to display
Optional Parameters:
--refID : the reference ID to read, defaults to print all
--summary : only print a summary - 1 line per reference.
--params : print the parameter settings
</pre>
 
=== Usage ===
./bam dumpIndex --bamIndex <bamIndexFile> [--refID <ref#>] [--summary] [--params]
 
=== Return Value ===
* 0: the BAM index file was processed successfully.
* non-0: the BAM index file was not processed successfully.
 
 
== readIndexedBam ==
The <code>readIndexedBam</code> option on the bam executable reads an indexed BAM file reference id by reference id -1 to the max reference id and writes it out as a SAM/BAM file.
 
=== Parameters ===
<pre>
Required Parameters:
inputFilename - path/name of the input BAM file
outputFile.sam/bam - path/name of the output file
bamIndexFile - path/name of the BAM index file
</pre>
 
=== Usage ===
./bam readIndexedBam <inputFilename> <outputFile.sam/bam> <bamIndexFile>
 
=== Return Value ===
* 0
 
== filter ==
 
The <code>filter</code> option on the bam executable filters the reads in a a SAM/BAM file. This option is documented at: [[Bam Executable: Filter]]
 
== diff ==
<span style="color:#D2691E">'''***Coming Soon***'''</span>
 
The <code>diff</code> option on the bam executable prints the difference between two coordinate sorted SAM/BAM files. This can be used to compare the outputs of running a SAM/BAM through different tools/versions of tools.
 
The <code>diff</code> tool compares records that have the same Read Name and Fragment (from the flag). If a matching ReadName & Fragment is not found, the record is considered to be different.
 
<code>diff</code> assumes the files are coordinate sorted and uses this assumption for determining how long to store a record before determining that the other file does not contain a matching ReadName/Fragment. If the files are not coordinate sorted, this logic does not work.
 
By default, just the chromosome/position and cigar are compared for each record.
 
Options are available to compare:
* sequence
* base quality
* specified tags
* turn off position comparison
* turn off cigar comparison
 
=== Parameters ===
<pre>
Required Parameters:
--in1 : first coordinate sorted SAM/BAM file to be diffed
--in2 : second coordinate sorted SAM/BAM file to be diffed
Optional Parameters:
--out : output filename, use .bam extension to output in SAM/BAM format instead of diff format.
In SAMBAM format there will be 3 output files:
1) the specified name with record diffs
2) specified name with _only_<in1>.sam/bam with records only in the in1 file
3) specified name with _only_<in2>.sam/bam with records only in the in2 file
--seq : diff the sequence bases.
--baseQual : diff the base qualities.
--tags : diff the specified Tags formatted as Tag:Type;Tag:Type;Tag:Type...
--noCigar : do not diff the the cigars.
--noPos : do not diff the positions.
--onlyDiffs : only print the fields that are different, otherwise for any diff all the fields that are compared are printed.
--recPoolSize : number of records to allow to be stored at a time, default value: 1000000
--posDiff : max base pair difference between possibly matching records100000
--noeof : do not expect an EOF block on a bam file.
--params : print the parameter settings
</pre>
 
=== Usage ===
./bam diff --in1 <inputFile> --in2 <inputFile> [--out <outputFile>] [--baseQual] [--tags <Tag:Type[;Tag:Type]*>] [--noCigar] [--noPos] [--onlyDiffs] [--recPoolSize <int>] [--posDiff <int>] [--noeof] [--params]
 
=== Return Value ===
* 0: all records are successfully read and written.
* non-0: an error occurred processing the parameters or reading one of the files.e
 
=== Output Format ===
2 Output Formats:
# Diff Format
# BAM Format
 
==== Diff Format ====
There are 2 types of differences.
* ReadName/Fragment combo is in one file, but not in the other file within the window set by recPoolSize & posDiff
* ReadName/Fragment combo is in both files, but at least one of the specified fields to diff is different
 
Each difference output consists of 2 or 3 lines. If the record only appears in one of the files, the diff is 2 lines, if it appears in both files, the diff is 3 lines.
 
The first line of the difference output is just the read name.
 
The 2nd and 3rd line (if present) begin with either a '<' or a '>'. If the record is from the first file (--in1), it begins with a '<'. If the record is from the 2nd file (--in2), it begins with a '>'.
 
The 2nd line is the flag followed by the diff'd fields from one of the records.
 
The 3rd line (if a matching record was found) is the flag followed by the diff'd fields from the matching record.
 
 
The diff'd record lines are tab separated, and are in the following order if --onlyDiffs is not specified:
* '<' or '>'
* flag
* chrom:pos (chromosome name ':' 1 based position) - if --noPos is not specified
* cigar - if --noCigar is not specified
* sequence - if --seq is specified
* base quality - if --baseQual is specified
* tag:type:value - for each tag:type specified in --tags
* ...
* tag:type:value
 
If <code>onlyDiffs</code> is specified, only the fields that are specified and are different get printed in lines 2 & 3.
 
===== Example Output =====
Command:
../bin/bam diff --in1 testFiles/testDiff1.sam --in2 testFiles/testDiff2.sam --seq --baseQual --tags "OP:i;MD:Z" --onlyDiffs --out results/diffOrderSam.log
 
Output:
<pre>
18:462+29M5I3M:F:295
< a1 1:78
> a1 1:74
1
> a1 1:70 3S1M1S ACGTN ;46>> OP:i:75 MD:Z:30A0C5
2
> a1 1:72 3S1M1S ACGTN ;47>> OP:i:75 MD:Z:30A0C5
ABC
> cd *:0 * * *
DEF
> cd *:0 * * *
</pre>
 
==== SAM/Bam Format ====
use .sam/.bam extension to output in SAM/BAM format instead of diff format.
 
In SAM/BAM format there will be 3 output files:
# the specified name with record diffs
# specified name with _only_<in1>.sam/bam with records only in the in1 file
# specified name with _only_<in2>.sam/bam with records only in the in2 file
 
When a record is found in both input files, but a difference is found, the record from the first file is written with additional tags to indicate the values from the second file, using the following tags:
* ZF - Flag
* ZP - Pos
* ZC - Cigar
* ZS - Sequence
* ZQ - Base Quality
* ZT - Tags
 
== readReference ==
The <code>readReference</code> option on the bam executable prints the specified region of the reference sequence in an easy to read format.
 
=== Parameters ===
<pre>
Required Parameters:
--refFile : the reference
--refName : the SAM/BAM reference Name to read
--start : inclusive 0-based start position (defaults to -1)
Required Length Parameter (one but not both needs to be specified):
--end : exclusive 0-based end position (defaults to -1: meaning til the end of the reference)
--numBases : number of bases from start to display
--params : print the parameter settings
</pre>
 
=== Usage ===
./bam readReference --refFile <referenceFilename> --refName <reference Name> --start <0 based start> --end <0 based end>|--numBases <number of bases> [--params]
 
=== Return Value ===
* 0: the reference file was successfully read.
* non-0: the reference file was not successfully read.
 
=== Example Output ===
<pre>
 
</pre>
 
== 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.
--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
</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.
 
Usage:
<pre>
./bam stats --in <inputFile> [--basic] [--qual] [--phred] [--baseQC <outputFileName>] [--maxNumReads <maxNum>] [--unmapped] [--bamIndex <bamIndexFile>] [--regionList <regFileName>] [--minMapQual <minMapQ>] [--dbsnp <dbsnpFile>] [--noeof] [--params]
</pre>
 
 
 
=== 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]
 
 
==== BaseQC ====
'''This capability is coming soon, so these notes may be updated prior to it being completed...'''
 
Do we print stats for positions where the reference base is 'N'?? (any special note for those? Qplot would not count them in the depth.)
 
The <code>baseQC</code> option generates the following statistics:
 
For each position, the following counts are incremented if:
# 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 the CIGAR for this position (other than clips at the beginning/end which are not counted, but deletions and skips are counted)
*TotalReads(e6) - # of reads that span this position.
*DupRate(%) - # of reads marked duplicate in the flag / TotalReads
*QCFailRate(%) - # of reads marked QC failure in the flag / TotalReads
*PairedReads(%) - # of reads marked paired in the flag / TotalReads
*ProperPaired(%) - # of reads marked paired AND proper paired in the flag / TotalReads
*MappedBases(e9) - # 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
 
 
For each position, the following counts are incremented if:
# a read spans the reference position (starts before or at this reference position and ends at or after this position)
# the read is NOT a duplicate, qc failure, unmapped, or mapped with a mapping quality less than the min
# the CIGAR for this position is a M/=/X (match/mismatch)
TBD - should it count if the read has a base of 'N'
*Depth - # of reads.
*Q20Bases(e9) - # of bases at this position with a base quality (from the read) of Q20 or higher.
*Q20BasesPct(%) - Q20Bases / Depth