picard.analysis

Class CollectAlignmentSummaryMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.SinglePassSamProgram

picard.analysis.CollectAlignmentSummaryMetrics

public class CollectAlignmentSummaryMetrics
extends SinglePassSamProgram

A command line tool to read a BAM file and produce standard alignment metrics that would be applicable to any alignment. Metrics to include, but not limited to:

• Total number of reads (total, period, no exclusions)
• Total number of PF reads (PF == does not fail vendor check flag)
• Number of PF noise reads (does not fail vendor check and has noise attr set)
• Total aligned PF reads (any PF read that has a sequence and position)
• High quality aligned PF reads (high quality == mapping quality >= 20)
• High quality aligned PF bases (actual aligned bases, calculate off alignment blocks)
• High quality aligned PF Q20 bases (subset of above where base quality >= 20)
• Median mismatches in HQ aligned PF reads (how many aligned bases != ref on average)
• Reads aligned in pairs (vs. reads aligned with mate unaligned/not present)
• Read length (how to handle mixed lengths?)
• Bad Cycles - how many machine cycles yielded combined no-call and mismatch rates of >= 80%
• Strand balance - reads mapped to positive strand / total mapped reads

Metrics are written for the first read of a pair, the second read, and combined for the pair. Chimeras are identified if any of the of following criteria are met:

• the insert size is larger than MAX_INSERT_SIZE
• the ends of a pair map to different contigs
• the paired end orientation is different that the expected orientation
• the read contains an SA tag (chimeric alignment)

Author:

Doug Voet (dvoet at broadinstitute dot org)

Field Summary

Fields

Modifier and Type	Field and Description
java.util.List<java.lang.String>	ADAPTER_SEQUENCE
java.util.Set<htsjdk.samtools.SamPairUtil.PairOrientation>	EXPECTED_PAIR_ORIENTATIONS
boolean	IS_BISULFITE_SEQUENCED
int	MAX_INSERT_SIZE
java.util.Set<MetricAccumulationLevel>	METRIC_ACCUMULATION_LEVEL
java.io.File	REFERENCE_SEQUENCE

Fields inherited from class picard.analysis.SinglePassSamProgram

ASSUME_SORTED, INPUT, OUTPUT, STOP_AFTER

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CollectAlignmentSummaryMetrics()

Method Summary

Modifier and Type	Method and Description
protected void	acceptRead(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref) Should be implemented by subclasses to accept SAMRecords one at a time.
protected void	finish() Should be implemented by subclasses to do one-time finalization work.
static void	main(java.lang.String[] argv) Required main method implementation.
protected void	setup(htsjdk.samtools.SAMFileHeader header, java.io.File samFile) Should be implemented by subclasses to do one-time initialization work.
protected int	testDoWork() Silly method that is necessary to give unit test access to call doWork()

Methods inherited from class picard.analysis.SinglePassSamProgram

doWork, makeItSo, usesNoRefReads

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

MAX_INSERT_SIZE

@Option(doc="Paired-end reads above this insert size will be considered chimeric along with inter-chromosomal pairs.")
public int MAX_INSERT_SIZE

EXPECTED_PAIR_ORIENTATIONS

@Option(doc="Paired-end reads that do not have this expected orientation will be considered chimeric.")
public java.util.Set<htsjdk.samtools.SamPairUtil.PairOrientation> EXPECTED_PAIR_ORIENTATIONS

ADAPTER_SEQUENCE

@Option(doc="List of adapter sequences to use when processing the alignment metrics.")
public java.util.List<java.lang.String> ADAPTER_SEQUENCE

METRIC_ACCUMULATION_LEVEL

@Option(shortName="LEVEL",
        doc="The level(s) at which to accumulate metrics.")
public java.util.Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL

IS_BISULFITE_SEQUENCED

@Option(shortName="BS",
        doc="Whether the SAM or BAM file consists of bisulfite sequenced reads.")
public boolean IS_BISULFITE_SEQUENCED

REFERENCE_SEQUENCE

@Option(shortName="R",
        doc="Reference sequence file. Note that while this argument isn\'t required, without it only a small subset of the metrics will be calculated. Note also that if a reference sequence is provided, it must be accompanied by a sequence dictionary.",
        optional=true,
        overridable=true)
public java.io.File REFERENCE_SEQUENCE

Constructor Detail

CollectAlignmentSummaryMetrics

public CollectAlignmentSummaryMetrics()

Method Detail

main

public static void main(java.lang.String[] argv)

Required main method implementation.

testDoWork

protected final int testDoWork()

Silly method that is necessary to give unit test access to call doWork()

setup

protected void setup(htsjdk.samtools.SAMFileHeader header,
                     java.io.File samFile)

Description copied from class: SinglePassSamProgram

Should be implemented by subclasses to do one-time initialization work.

Specified by:

setup in class SinglePassSamProgram

acceptRead

protected void acceptRead(htsjdk.samtools.SAMRecord rec,
                          htsjdk.samtools.reference.ReferenceSequence ref)

Description copied from class: SinglePassSamProgram

Should be implemented by subclasses to accept SAMRecords one at a time. If the read has a reference sequence and a reference sequence file was supplied to the program it will be passed as 'ref'. Otherwise 'ref' may be null.

Specified by:

acceptRead in class SinglePassSamProgram

finish

protected void finish()

Description copied from class: SinglePassSamProgram

Should be implemented by subclasses to do one-time finalization work.

Specified by:

finish in class SinglePassSamProgram