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

Author:

Tim Fennell, George Grant

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
boolean	MISSING_SITES_HOM_REF
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

Modifier and Type	Method and Description
static void	addMissingTruthAndMissingCallStates(double numVariants, long intervalBaseCount, GenotypeConcordanceCounts counter) Method to add missing sites that are KNOWN to be HOM_REF in the case of the NIST truth data set.
static boolean	classifyVariants(java.util.Optional<htsjdk.variant.variantcontext.VariantContext> truthContext, java.lang.String truthSample, java.util.Optional<htsjdk.variant.variantcontext.VariantContext> callContext, java.lang.String callSample, int minGq, int minDp)
static boolean	classifyVariants(java.util.Optional<htsjdk.variant.variantcontext.VariantContext> truthContext, java.lang.String truthSample, java.util.Optional<htsjdk.variant.variantcontext.VariantContext> callContext, java.lang.String callSample, java.util.Optional<GenotypeConcordanceCounts> snpCounter, java.util.Optional<GenotypeConcordanceCounts> indelCounter, int minGq, int minDp) Attempts to determine the concordance state given the truth and all variant context and optionally increments the genotype concordance count for the given variant type (SNP or INDEL).
protected java.lang.String[]	customCommandLineValidation() Put any custom command-line validation in an override of this method.
static GenotypeConcordanceStates.TruthAndCallStates	determineState(htsjdk.variant.variantcontext.VariantContext truthContext, java.lang.String truthSample, htsjdk.variant.variantcontext.VariantContext callContext, java.lang.String callSample, int minGq, int minDp) A method to determine the truth and call states for a pair of variant contexts representing truth and call.
protected int	doWork() Do the work after command line has been parsed.
GenotypeConcordanceCounts	getIndelCounter()
GenotypeConcordanceCounts	getSnpCounter()
static void	main(java.lang.String[] args)
static void	outputDetailMetricsFile(htsjdk.variant.variantcontext.VariantContext.Type variantType, htsjdk.samtools.metrics.MetricsFile<GenotypeConcordanceDetailMetrics,?> genotypeConcordanceDetailMetricsFile, GenotypeConcordanceCounts counter, java.lang.String truthSampleName, java.lang.String callSampleName, boolean missingSitesHomRef, boolean outputAllRows) Outputs the detailed statistics tables for SNP and Indel match categories.

Methods inherited from class picard.cmdline.CommandLineProgram

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 <OUTPUT>.genotype_concordance_summary_metrics  and <OUTPUT>.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.  Note - if intervals are specified, the VCF files must be indexed.")
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

MISSING_SITES_HOM_REF

@Option(shortName="MISSING_HOM",
        doc="Default is false, which follows the GA4GH Scheme. If true, missing sites in the truth set will be treated as HOM_REF sites and sites missing in both the truth and call sets will be true negatives. Useful when hom ref sites are left out of the truth set. This flag can only be used with a high confidence interval list.")
public boolean MISSING_SITES_HOM_REF

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)

customCommandLineValidation

protected java.lang.String[] customCommandLineValidation()

Description copied from class: CommandLineProgram

Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.

Overrides:

customCommandLineValidation in class CommandLineProgram

Returns:

null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.

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.

classifyVariants

public static boolean classifyVariants(java.util.Optional<htsjdk.variant.variantcontext.VariantContext> truthContext,
                                       java.lang.String truthSample,
                                       java.util.Optional<htsjdk.variant.variantcontext.VariantContext> callContext,
                                       java.lang.String callSample,
                                       int minGq,
                                       int minDp)

classifyVariants

public static boolean classifyVariants(java.util.Optional<htsjdk.variant.variantcontext.VariantContext> truthContext,
                                       java.lang.String truthSample,
                                       java.util.Optional<htsjdk.variant.variantcontext.VariantContext> callContext,
                                       java.lang.String callSample,
                                       java.util.Optional<GenotypeConcordanceCounts> snpCounter,
                                       java.util.Optional<GenotypeConcordanceCounts> indelCounter,
                                       int minGq,
                                       int minDp)

Attempts to determine the concordance state given the truth and all variant context and optionally increments the genotype concordance count for the given variant type (SNP or INDEL). This will ignore cases where an indel was found in the truth and a SNP was found in the call, and vice versa. We typically fail to classify Mixed, Symbolic variants, or MNPs.

Parameters:

truthContext - A variant context representing truth

truthSample - The name of the truth sample

callContext - A variant context representing the call

callSample - The name of the call sample

snpCounter - optionally a place to increment the counts for SNP truth/call states

indelCounter - optionally a place to increment the counts for INDEL truth/call states

minGq - Threshold for filtering by genotype attribute GQ

minDp - Threshold for filtering by genotype attribute DP

Returns:

true if the concordance state could be classified.

addMissingTruthAndMissingCallStates

public static void addMissingTruthAndMissingCallStates(double numVariants,
                                                       long intervalBaseCount,
                                                       GenotypeConcordanceCounts counter)

Method to add missing sites that are KNOWN to be HOM_REF in the case of the NIST truth data set.

outputDetailMetricsFile

public static void outputDetailMetricsFile(htsjdk.variant.variantcontext.VariantContext.Type variantType,
                                           htsjdk.samtools.metrics.MetricsFile<GenotypeConcordanceDetailMetrics,?> genotypeConcordanceDetailMetricsFile,
                                           GenotypeConcordanceCounts counter,
                                           java.lang.String truthSampleName,
                                           java.lang.String callSampleName,
                                           boolean missingSitesHomRef,
                                           boolean outputAllRows)

Outputs the detailed statistics tables for SNP and Indel match categories.

determineState

public static final GenotypeConcordanceStates.TruthAndCallStates determineState(htsjdk.variant.variantcontext.VariantContext truthContext,
                                                                                java.lang.String truthSample,
                                                                                htsjdk.variant.variantcontext.VariantContext callContext,
                                                                                java.lang.String callSample,
                                                                                int minGq,
                                                                                int minDp)

A method to determine the truth and call states for a pair of variant contexts representing truth and call. A variety of variant and genotype-level checks are first used to determine if either of the the variant contexts are filtered and after that a comparison of the called genotype alleles to determine appropriate truth and call state Note that this method does NOT check for SNP versus Indel. It is assumed that that check is done by the caller and the results of this method are stored by SNP/Indel. Note that if a variant context has BOTH GQ and DP less than the specified threshold, then it will be of Truth/Call State LOW_GQ

Parameters:

truthContext - A variant context representing truth

truthSample - The name of the truth sample

callContext - A variant context representing the call

callSample - The name of the call sample

minGq - Threshold for filtering by genotype attribute GQ

minDp - Threshold for filtering by genotype attribute DP

Returns:

TruthAndCallStates object containing the TruthState and CallState determined here.