picard.analysis.replicates

Class CollectIndependentReplicateMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.replicates.CollectIndependentReplicateMetrics

@DocumentedFeature
 @BetaFeature
public class CollectIndependentReplicateMetrics
extends CommandLineProgram

A CLP that, given a BAM and a VCF with genotypes of the same sample, estimates the rate of independent replication of reads within the bam. That is, it estimates the fraction of the reads which look like duplicates (in the MarkDuplicates sense of the word) but are actually independent observations of the data. In the presence of Unique Molecular Identifiers (UMIs), various metrics are collected regarding the utility of the UMI's for the purpose of increasing coverage.

The estimation is based on duplicate-sets of size 2 and 3 and gives separate estimates from each. The assumption is that the duplication rate (biological or otherwise) is independent of the duplicate-set size. A significant difference between the two rates may be an indication that this assumption is incorrect.

The duplicate sets are found using the mate-cigar tag (MC) which is added by MergeBamAlignment , or FixMateInformation. This program will not work without the MC tag.

Explanation of the calculation behind the estimation can be found in the IndependentReplicateMetric class.

The calculation Assumes a diploid organism (more accurately, assumes that only two alleles can appear at a HET site and that these two alleles will appear at equal probabilities. It requires as input a VCF with genotypes for the sample in question. NOTE: This class is very much in alpha stage, and still under heavy development (feel free to join!)

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	BARCODE_BQ
java.lang.String	BARCODE_TAG
java.io.File	INPUT
java.io.File	MATRIX_OUTPUT
java.lang.Integer	MINIMUM_BARCODE_BQ
java.lang.Integer	MINIMUM_BQ
java.lang.Integer	MINIMUM_GQ
java.lang.Integer	MINIMUM_MQ
java.io.File	OUTPUT
java.lang.String	SAMPLE
java.lang.Integer	STOP_AFTER
java.io.File	VCF

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CollectIndependentReplicateMetrics()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

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

Field Detail

INPUT

@Argument(shortName="I",
          doc="Input (indexed) BAM file.")
public java.io.File INPUT

OUTPUT

@Argument(shortName="O",
          doc="Write metrics to this file")
public java.io.File OUTPUT

MATRIX_OUTPUT

@Argument(shortName="MO",
          doc="Write the confusion matrix (of UMIs) to this file",
          optional=true)
public java.io.File MATRIX_OUTPUT

VCF

@Argument(shortName="V",
          doc="Input VCF file")
public java.io.File VCF

MINIMUM_GQ

@Argument(shortName="GQ",
          doc="minimal value for the GQ field in the VCF to use variant site.",
          optional=true)
public java.lang.Integer MINIMUM_GQ

MINIMUM_MQ

@Argument(shortName="MQ",
          doc="minimal value for the mapping quality of the reads to be used in the estimation.",
          optional=true)
public java.lang.Integer MINIMUM_MQ

MINIMUM_BQ

@Argument(shortName="BQ",
          doc="minimal value for the base quality of a base to be used in the estimation.",
          optional=true)
public java.lang.Integer MINIMUM_BQ

SAMPLE

@Argument(shortName="ALIAS",
          doc="Name of sample to look at in VCF. Can be omitted if VCF contains only one sample.",
          optional=true)
public java.lang.String SAMPLE

STOP_AFTER

@Argument(doc="Number of sets to examine before stopping.",
          optional=true)
public java.lang.Integer STOP_AFTER

BARCODE_TAG

@Argument(doc="Barcode SAM tag.",
          optional=true)
public java.lang.String BARCODE_TAG

BARCODE_BQ

@Argument(doc="Barcode Quality SAM tag.",
          optional=true)
public java.lang.String BARCODE_BQ

MINIMUM_BARCODE_BQ

@Argument(shortName="MBQ",
          doc="minimal value for the base quality of all the bases in a molecular barcode, for it to be used.",
          optional=true)
public java.lang.Integer MINIMUM_BARCODE_BQ

Constructor Detail

CollectIndependentReplicateMetrics

public CollectIndependentReplicateMetrics()

Method Detail

doWork

protected int doWork()

Description copied from class: CommandLineProgram

Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.