picard.fingerprint

Class FingerprintChecker

java.lang.Object

picard.fingerprint.FingerprintChecker

public class FingerprintChecker
extends java.lang.Object

Major class that coordinates the activities involved in comparing genetic fingerprint data whether the source is from a genotyping platform or derived from sequence data.

Field Summary

Fields

Modifier and Type	Field and Description
static double	DEFAULT_GENOTYPING_ERROR_RATE
static int	DEFAULT_MAXIMAL_PL_DIFFERENCE
static int	DEFAULT_MINIMUM_BASE_QUALITY
static int	DEFAULT_MINIMUM_MAPPING_QUALITY

Constructor Summary

Constructors

Constructor and Description
FingerprintChecker(java.io.File haplotypeData) Creates a fingerprint checker that will work with the set of haplotypes stored in the supplied file.
FingerprintChecker(HaplotypeMap haplotypes) Creates a fingerprint checker that will work with the set of haplotyped provided.

Method Summary

Modifier and Type	Method and Description
static MatchResults	calculateMatchResults(Fingerprint observedFp, Fingerprint expectedFp) Compares two fingerprints and calculates a MatchResults object which contains detailed information about the match (or mismatch) between fingerprints including the LOD score for whether or not the two are likely from the same sample.
static MatchResults	calculateMatchResults(Fingerprint observedFp, Fingerprint expectedFp, double minPExpected, double pLoH) Compares two fingerprints and calculates a MatchResults object which contains detailed information about the match (or mismatch) between fingerprints including the LOD score for whether or not the two are likely from the same sample.
java.util.List<FingerprintResults>	checkFingerprints(java.util.List<java.io.File> samFiles, java.util.List<java.io.File> genotypeFiles, java.lang.String specificSample, boolean ignoreReadGroups) Top level method to take a set of one or more SAM files and one or more Genotype files and compare each read group in each SAM file to each set of fingerprint genotypes.
java.util.List<FingerprintResults>	checkFingerprints(java.util.List<java.io.File> observedGenotypeFiles, java.util.List<java.io.File> expectedGenotypeFiles, java.lang.String observedSample, java.lang.String expectedSample) Top level method to take a set of one or more observed genotype (VCF) files and one or more expected genotype (VCF) files and compare one or more sample in the observed genotype file with one or more in the expected file and generate results for each set.
java.util.Map<FingerprintIdDetails,Fingerprint>	fingerprintFiles(java.util.Collection<java.io.File> files, int threads, int waitTime, java.util.concurrent.TimeUnit waitTimeUnit) Fingerprints one or more SAM/BAM/VCF files at all available loci within the haplotype map, using multiple threads to speed up the processing.
java.util.Map<FingerprintIdDetails,Fingerprint>	fingerprintSamFile(java.io.File samFile, htsjdk.samtools.util.IntervalList loci) Generates a Fingerprint per read group in the supplied SAM file using the loci provided in the interval list.
java.util.Map<FingerprintIdDetails,Fingerprint>	fingerprintVcf(java.io.File vcfFile)
htsjdk.samtools.SAMFileHeader	getHeader()
htsjdk.samtools.util.IntervalList	getLociToGenotype(java.util.Collection<Fingerprint> fingerprints) Takes a set of fingerprints and returns an IntervalList containing all the loci that can be productively examined in sequencing data to compare to one or more of the fingerprints.
htsjdk.samtools.ValidationStringency	getValidationStringency()
java.util.Map<java.lang.String,Fingerprint>	identifyContaminant(java.io.File samFile, double contamination, int locusMaxReads) Generates a per-sample Fingerprint for the contaminant in the supplied SAM file.
static boolean	isUsableSnp(htsjdk.variant.variantcontext.VariantContext ctx) Quick method to check and see if the variant context represents a usable SNP variant.
java.util.Map<java.lang.String,Fingerprint>	loadFingerprints(java.io.File fingerprintFile, java.lang.String specificSample) Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
java.util.Map<java.lang.String,Fingerprint>	loadFingerprintsFromIndexedVcf(java.io.File fingerprintFile, java.lang.String specificSample) Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
java.util.Map<java.lang.String,Fingerprint>	loadFingerprintsFromNonIndexedVcf(java.io.File fingerprintFile, java.lang.String specificSample) Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
protected static <T> java.util.List<T>	randomSublist(java.util.List<T> list, int n) A small utility function to choose n random elements (un-shuffled) from a list
void	setAllowDuplicateReads(boolean allowDuplicateReads) Sets whether duplicate reads should be allowed when calling genotypes from SAM files.
void	setGenotypingErrorRate(double genotypingErrorRate) Sets the assumed genotyping error rate used when accurate error rates are not available.
void	setmaximalPLDifference(int maximalPLDifference) Sets the maximal difference in PL scores considered when reading PLs from a VCF.
void	setMinimumBaseQuality(int minimumBaseQuality) Sets the minimum base quality for bases used when computing a fingerprint from sequence data.
void	setMinimumMappingQuality(int minimumMappingQuality) Sets the minimum mapping quality for reads used when computing fingerprints from sequence data.
void	setpLossofHet(double pLossofHet)
void	setValidationStringency(htsjdk.samtools.ValidationStringency validationStringency)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_GENOTYPING_ERROR_RATE

public static final double DEFAULT_GENOTYPING_ERROR_RATE

See Also:

Constant Field Values

DEFAULT_MINIMUM_MAPPING_QUALITY

public static final int DEFAULT_MINIMUM_MAPPING_QUALITY

See Also:

Constant Field Values

DEFAULT_MINIMUM_BASE_QUALITY

public static final int DEFAULT_MINIMUM_BASE_QUALITY

See Also:

Constant Field Values

DEFAULT_MAXIMAL_PL_DIFFERENCE

public static final int DEFAULT_MAXIMAL_PL_DIFFERENCE

See Also:

Constant Field Values

Constructor Detail

FingerprintChecker

public FingerprintChecker(java.io.File haplotypeData)

Creates a fingerprint checker that will work with the set of haplotypes stored in the supplied file.

FingerprintChecker

public FingerprintChecker(HaplotypeMap haplotypes)

Creates a fingerprint checker that will work with the set of haplotyped provided.

Method Detail

getValidationStringency

public htsjdk.samtools.ValidationStringency getValidationStringency()

setValidationStringency

public void setValidationStringency(htsjdk.samtools.ValidationStringency validationStringency)

setMinimumBaseQuality

public void setMinimumBaseQuality(int minimumBaseQuality)

Sets the minimum base quality for bases used when computing a fingerprint from sequence data.

setMinimumMappingQuality

public void setMinimumMappingQuality(int minimumMappingQuality)

Sets the minimum mapping quality for reads used when computing fingerprints from sequence data.

setGenotypingErrorRate

public void setGenotypingErrorRate(double genotypingErrorRate)

Sets the assumed genotyping error rate used when accurate error rates are not available.

setmaximalPLDifference

public void setmaximalPLDifference(int maximalPLDifference)

Sets the maximal difference in PL scores considered when reading PLs from a VCF.

getHeader

public htsjdk.samtools.SAMFileHeader getHeader()

setAllowDuplicateReads

public void setAllowDuplicateReads(boolean allowDuplicateReads)

Sets whether duplicate reads should be allowed when calling genotypes from SAM files. This is useful when comparing read groups within a SAM file and individual read groups show artifactually high duplication (e.g. a single-ended read group mixed in with paired-end read groups).

Parameters:

allowDuplicateReads - should fingerprinting use duplicate reads?

setpLossofHet

public void setpLossofHet(double pLossofHet)

loadFingerprints

public java.util.Map<java.lang.String,Fingerprint> loadFingerprints(java.io.File fingerprintFile,
                                                                    java.lang.String specificSample)

Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.

Parameters:

fingerprintFile - - VCF file containing genotypes for one or more samples

specificSample - - null to load genotypes for all samples contained in the file or the name of an individual sample to load (and exclude all others).

Returns:

a Map of Sample name to Fingerprint

loadFingerprintsFromNonIndexedVcf

public java.util.Map<java.lang.String,Fingerprint> loadFingerprintsFromNonIndexedVcf(java.io.File fingerprintFile,
                                                                                     java.lang.String specificSample)

Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.

Parameters:

fingerprintFile - - VCF file containing genotypes for one or more samples

specificSample - - null to load genotypes for all samples contained in the file or the name of an individual sample to load (and exclude all others).

Returns:

a Map of Sample name to Fingerprint

loadFingerprintsFromIndexedVcf

public java.util.Map<java.lang.String,Fingerprint> loadFingerprintsFromIndexedVcf(java.io.File fingerprintFile,
                                                                                  java.lang.String specificSample)

Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.

Parameters:

fingerprintFile - - VCF file containing genotypes for one or more samples

specificSample - - null to load genotypes for all samples contained in the file or the name of an individual sample to load (and exclude all others).

Returns:

a Map of Sample name to Fingerprint

isUsableSnp

public static boolean isUsableSnp(htsjdk.variant.variantcontext.VariantContext ctx)

Quick method to check and see if the variant context represents a usable SNP variant. Unfortunately ctx.isSnp doesn't always work if the genotype(s) are all monomorphic and the alternate allele isn't listed.

getLociToGenotype

public htsjdk.samtools.util.IntervalList getLociToGenotype(java.util.Collection<Fingerprint> fingerprints)

Takes a set of fingerprints and returns an IntervalList containing all the loci that can be productively examined in sequencing data to compare to one or more of the fingerprints.

fingerprintVcf

public java.util.Map<FingerprintIdDetails,Fingerprint> fingerprintVcf(java.io.File vcfFile)

fingerprintSamFile

public java.util.Map<FingerprintIdDetails,Fingerprint> fingerprintSamFile(java.io.File samFile,
                                                                          htsjdk.samtools.util.IntervalList loci)

Generates a Fingerprint per read group in the supplied SAM file using the loci provided in the interval list.

identifyContaminant

public java.util.Map<java.lang.String,Fingerprint> identifyContaminant(java.io.File samFile,
                                                                       double contamination,
                                                                       int locusMaxReads)

Generates a per-sample Fingerprint for the contaminant in the supplied SAM file. Data is aggregated by sample, not read-group.

randomSublist

protected static <T> java.util.List<T> randomSublist(java.util.List<T> list,
                                                     int n)

A small utility function to choose n random elements (un-shuffled) from a list

Parameters:

list - A list of elements

n - a number of elements requested from list

Returns:

a list of n randomly chosen (but in the original order) elements from list. If the list has less than n elements it is returned in its entirety.

fingerprintFiles

public java.util.Map<FingerprintIdDetails,Fingerprint> fingerprintFiles(java.util.Collection<java.io.File> files,
                                                                        int threads,
                                                                        int waitTime,
                                                                        java.util.concurrent.TimeUnit waitTimeUnit)

Fingerprints one or more SAM/BAM/VCF files at all available loci within the haplotype map, using multiple threads to speed up the processing.

checkFingerprints

public java.util.List<FingerprintResults> checkFingerprints(java.util.List<java.io.File> samFiles,
                                                            java.util.List<java.io.File> genotypeFiles,
                                                            java.lang.String specificSample,
                                                            boolean ignoreReadGroups)

Top level method to take a set of one or more SAM files and one or more Genotype files and compare each read group in each SAM file to each set of fingerprint genotypes.

Parameters:

samFiles - the list of SAM files to fingerprint

genotypeFiles - the list of genotype files from which to pull fingerprint genotypes

specificSample - an optional single sample who's genotypes to load from the supplied files

ignoreReadGroups - aggregate data into one fingerprint per file, instead of splitting by RG

checkFingerprints

public java.util.List<FingerprintResults> checkFingerprints(java.util.List<java.io.File> observedGenotypeFiles,
                                                            java.util.List<java.io.File> expectedGenotypeFiles,
                                                            java.lang.String observedSample,
                                                            java.lang.String expectedSample)

Top level method to take a set of one or more observed genotype (VCF) files and one or more expected genotype (VCF) files and compare one or more sample in the observed genotype file with one or more in the expected file and generate results for each set.

Parameters:

observedGenotypeFiles - The list of genotype files containing observed calls, from which to pull fingerprint genotypes

expectedGenotypeFiles - The list of genotype files containing expected calls, from which to pull fingerprint genotypes

observedSample - an optional single sample whose genotypes to load from the observed genotype file (if null, use all)

expectedSample - an optional single sample whose genotypes to load from the expected genotype file (if null, use all)

calculateMatchResults

public static MatchResults calculateMatchResults(Fingerprint observedFp,
                                                 Fingerprint expectedFp,
                                                 double minPExpected,
                                                 double pLoH)

Compares two fingerprints and calculates a MatchResults object which contains detailed information about the match (or mismatch) between fingerprints including the LOD score for whether or not the two are likely from the same sample. If comparing sequencing data to genotype data then the sequencing data should be passed as the observedFp and the genotype data as the expectedFp in order to get the best output. In the cases where the most likely genotypes from the two fingerprints do not match the lExpectedSample is Max(actualpExpectedSample, minPExpected).

calculateMatchResults

public static MatchResults calculateMatchResults(Fingerprint observedFp,
                                                 Fingerprint expectedFp)

Compares two fingerprints and calculates a MatchResults object which contains detailed information about the match (or mismatch) between fingerprints including the LOD score for whether or not the two are likely from the same sample. If comparing sequencing data to genotype data then the sequencing data should be passed as the observedFp and the genotype data as the expectedFp in order to get the best output.