picard.vcf

Class GenotypeConcordance

java.lang.Object

picard.cmdline.CommandLineProgram

picard.vcf.GenotypeConcordance

public class GenotypeConcordance
extends CommandLineProgram

Calculates the concordance between genotype data for two samples in two different VCFs - one being considered the truth (or reference) the other being the call. The concordance is broken into separate results sections for SNPs and indels. Summary and detailed statistics are reported

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	CALL_SAMPLE
java.io.File	CALL_VCF
static java.lang.String	CONTINGENCY_METRICS_FILE_EXTENSION
static java.lang.String	DETAILED_METRICS_FILE_EXTENSION
protected GenotypeConcordanceCounts	indelCounter
boolean	INTERSECT_INTERVALS
java.util.List<java.io.File>	INTERVALS
int	MIN_DP
int	MIN_GQ
java.io.File	OUTPUT
boolean	OUTPUT_ALL_ROWS
protected GenotypeConcordanceCounts	snpCounter
static java.lang.String	SUMMARY_METRICS_FILE_EXTENSION
java.lang.String	TRUTH_SAMPLE
java.io.File	TRUTH_VCF
boolean	USE_VCF_INDEX

Fields inherited from class picard.cmdline.CommandLineProgram

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

Constructor Summary

Constructors

Constructor and Description
GenotypeConcordance()

Method Summary

Methods

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.
GenotypeConcordanceCounts	getIndelCounter()
GenotypeConcordanceCounts	getSnpCounter()
static void	main(java.lang.String[] args)

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

TRUTH_VCF

@Option(shortName="TV",
        doc="The VCF containing the truth sample")
public java.io.File TRUTH_VCF

CALL_VCF

@Option(shortName="CV",
        doc="The VCF containing the call sample")
public java.io.File CALL_VCF

OUTPUT

@Option(shortName="O",
        doc="Basename for the two metrics files that are to be written. Resulting files will be 
.genotype_concordance_summary_metrics  and 
.genotype_concordance_detail_metrics.")
public java.io.File OUTPUT

TRUTH_SAMPLE

@Option(shortName="TS",
        doc="The name of the truth sample within the truth VCF")
public java.lang.String TRUTH_SAMPLE

CALL_SAMPLE

@Option(shortName="CS",
        doc="The name of the call sample within the call VCF")
public java.lang.String CALL_SAMPLE

INTERVALS

@Option(doc="One or more interval list files that will be used to limit the genotype concordance.")
public java.util.List<java.io.File> INTERVALS

INTERSECT_INTERVALS

@Option(doc="If true, multiple interval lists will be intersected. If false multiple lists will be unioned.")
public boolean INTERSECT_INTERVALS

MIN_GQ

@Option(doc="Genotypes below this genotype quality will have genotypes classified as LowGq.")
public int MIN_GQ

MIN_DP

@Option(doc="Genotypes below this depth will have genotypes classified as LowDp.")
public int MIN_DP

OUTPUT_ALL_ROWS

@Option(doc="If true, output all rows in detailed statistics even when count == 0.  When false only output rows with non-zero counts.")
public boolean OUTPUT_ALL_ROWS

USE_VCF_INDEX

@Option(doc="If true, use the VCF index, else iterate over the entire VCF.",
        optional=true)
public boolean USE_VCF_INDEX

SUMMARY_METRICS_FILE_EXTENSION

public static final java.lang.String SUMMARY_METRICS_FILE_EXTENSION

See Also:

Constant Field Values

DETAILED_METRICS_FILE_EXTENSION

public static final java.lang.String DETAILED_METRICS_FILE_EXTENSION

See Also:

Constant Field Values

CONTINGENCY_METRICS_FILE_EXTENSION

public static final java.lang.String CONTINGENCY_METRICS_FILE_EXTENSION

See Also:

Constant Field Values

snpCounter

protected GenotypeConcordanceCounts snpCounter

indelCounter

protected GenotypeConcordanceCounts indelCounter

Constructor Detail

GenotypeConcordance

public GenotypeConcordance()

Method Detail

getSnpCounter

public GenotypeConcordanceCounts getSnpCounter()

getIndelCounter

public GenotypeConcordanceCounts getIndelCounter()

main

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

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.