| Line 18: |
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| | (It will be available without libStatGen in case you already have a downloaded version of libStatGen that you want to use. | | (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 are '''Coming Soon'''.
| + | Release downloads are '''Coming Soon'''. |
| | | | |
| | | | |
| Line 62: |
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| | | | |
| | The bam executable has the following functions. | | The bam executable has the following functions. |
| − | * [[C++ Executable: bam#validate|validate - Read and Validate a SAM/BAM file]] | + | * [[BamUtil: 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)]] | | * [[BamUtil: convert|convert - Read a SAM/BAM file and write as a SAM/BAM file (optionally converts between '=' & bases in the sequence)]] |
| − | * [[C++ Executable: bam#dumpHeader|dumpHeader - Print SAM/BAM header]] | + | * [[BamUtil: dumpHeader|dumpHeader - Print SAM/BAM header]] |
| − | * [[C++ Executable: bam#splitChromosome|splitChromosome - Split BAM by Chromosome]] | + | * [[BamUtil: splitChromosome|splitChromosome - Split BAM by Chromosome]] |
| − | * [[C++ Executable: bam#writeRegion|writeRegion - Write the alignments in the indexed BAM file that fall into the specified region]] | + | * [[BamUtil: writeRegion|writeRegion - Write the alignments in the indexed BAM file that fall into the specified region]] |
| − | * [[C++ Executable: bam#dumpRefInfo|dumpRefInfo - Print SAM/BAM Reference Information]] | + | * [[BamUtil: dumpRefInfo|dumpRefInfo - Print SAM/BAM Reference Information]] |
| − | * [[C++ Executable: bam#dumpIndex|dumpIndex - Dump a BAM index file into an easy to read text version]] | + | * [[BamUtil: dumpIndex|dumpIndex - Dump a BAM index file into an easy to read text version]] |
| − | * [[C++ Executable: 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]] | + | * [[BamUtil: 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++ Executable: 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]] | + | * [[BamUtil: 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++ Executable: bam#readReference|readReference - Print the reference string for the specified region]] | + | * [[BamUtil: readReference|readReference - Print the reference string for the specified region]] |
| − | * [[C++ Executable: bam#diff|diff - Print the diffs between 2 bams]] | + | * [[BamUtil: 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]]. | | This executable is built using [[C++ Library: libStatGen]]. |
| | | | |
| | Just running ./bam will print the Usage information for the bam executable. | | 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
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| − | *ProperPair - # of reads marked paired AND proper paired in the flag
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| − | *DuplicateReads - # of reads marked duplicate in the flag
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| − | *QCFailureReads - # of reads marked QC failure in the flag
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| − | *MappingRate(%) - # of reads marked mapped in the flag / TotalReads
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| − | *PairedReads(%) - # of reads marked paired in the flag / TotalReads
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| − | *ProperPair(%) - # of reads marked paired AND proper paired in the flag / TotalReads
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| − | *DupRate(%) - # of reads marked duplicate in the flag / TotalReads
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| − | *QCFailRate(%) - # of reads marked QC failure in the flag / TotalReads
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| − | *TotalBases - # of bases in all reads
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| − | *BasesInMappedReads - # of bases in reads marked mapped in the flag
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| − |
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| − |
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| − |
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| − | ==== Qual/Phred ====
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| − | Prints a count of the number of times each quality value appears in the file.
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| − | *<code>phred</code> Displays Quality as phred integers [0-93]
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| − | *<code>qual</code> Displays Quality as non-phred integers (phred + 33) [33-126]
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| − |
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| − |
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| − | ==== BaseQC ====
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| − | '''This capability is coming soon, so these notes may be updated prior to it being completed...'''
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| − |
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| − | 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.)
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| − |
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| − | The <code>baseQC</code> option generates the following statistics:
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| − |
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| − | For each position, the following counts are incremented if:
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| − | # a read spans the reference position (starts before or at this reference position and ends at or after this position)
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| − | # regardless of duplicate/qc failure/unmapped/mapping quality
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| − | # regardless of the CIGAR for this position (other than clips at the beginning/end which are not counted, but deletions and skips are counted)
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| − | *TotalReads(e6) - # of reads that span this position.
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| − | *DupRate(%) - # of reads marked duplicate in the flag / TotalReads
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| − | *QCFailRate(%) - # of reads marked QC failure in the flag / TotalReads
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| − | *PairedReads(%) - # of reads marked paired in the flag / TotalReads
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| − | *ProperPaired(%) - # of reads marked paired AND proper paired in the flag / TotalReads
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| − | *MappedBases(e9) - # of reads marked mapped in the flag
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| − | *MappingRate(%) - # of reads marked mapped in the flag / TotalReads
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| − | *ZeroMapQual(%) - # of reads marked mapped in the flag AND have a Mapping Quality of 0 / TotalReads
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| − | *MapQual<10(%) - # of reads marked mapped in the flag AND have a Mapping Quality < 10 / TotalReads
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| − | *MapRate_MQpass(%) - # of reads marked mapped in the flag AND have a Mapping Quality >= a minimum Mapping Quality / TotalReads
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| − |
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| − |
| |
| − | For each position, the following counts are incremented if:
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| − | # a read spans the reference position (starts before or at this reference position and ends at or after this position)
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| − | # the read is NOT a duplicate, qc failure, unmapped, or mapped with a mapping quality less than the min
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| − | # the CIGAR for this position is a M/=/X (match/mismatch)
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| − | TBD - should it count if the read has a base of 'N'
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| − | *Depth - # of reads.
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| − | *Q20Bases(e9) - # of bases at this position with a base quality (from the read) of Q20 or higher.
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| − | *Q20BasesPct(%) - Q20Bases / Depth
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