picard.fingerprint

Class CrosscheckReadGroupFingerprints

java.lang.Object

picard.cmdline.CommandLineProgram

picard.fingerprint.CrosscheckReadGroupFingerprints

public class CrosscheckReadGroupFingerprints
extends CommandLineProgram

Program to check that all read groups within the set of BAM files appear to come from the same individual.

Author:

Tim Fennell

Field Summary

Fields

Modifier and Type	Field and Description
boolean	ALLOW_DUPLICATE_READS
boolean	CROSSCHECK_LIBRARIES
boolean	CROSSCHECK_SAMPLES
int	EXIT_CODE_WHEN_MISMATCH
boolean	EXPECT_ALL_READ_GROUPS_TO_MATCH
static java.lang.String	EXPECTED_MATCH
static java.lang.String	EXPECTED_MISMATCH
double	GENOTYPING_ERROR_RATE
java.io.File	HAPLOTYPE_MAP
java.util.List<java.io.File>	INPUT
double	LOD_THRESHOLD
double	LOSS_OF_HET_RATE
int	NUM_THREADS
java.io.File	OUTPUT
boolean	OUTPUT_ERRORS_ONLY
static java.lang.String	UNEXPECTED_MATCH
static java.lang.String	UNEXPECTED_MISMATCH

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
CrosscheckReadGroupFingerprints()

Method Summary

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

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

INPUT

@Option(shortName="I",
        doc="One or more input BAM files (or lists of BAM files) to compare fingerprints for.")
public java.util.List<java.io.File> INPUT

OUTPUT

@Option(shortName="O",
        optional=true,
        doc="Optional output file to write metrics to. Default is to write to stdout.")
public java.io.File OUTPUT

HAPLOTYPE_MAP

@Option(shortName="H",
        doc="The file of haplotype data to use to pick SNPs to fingerprint")
public java.io.File HAPLOTYPE_MAP

LOD_THRESHOLD

@Option(shortName="LOD",
        doc="If any two read groups match with a LOD score lower than the threshold the program will exit with a non-zero code to indicate error. 0 means equal probability the read groups match vs. come from different individuals, negative numbers mean N logs more likely that the read groups are from different individuals and positive numbers mean N logs more likely that the read groups are from the sample individual.")
public double LOD_THRESHOLD

CROSSCHECK_SAMPLES

@Option(doc="Instead of producing the normal comparison of read-groups, roll fingerprints up to the sample level and print out a sample x sample matrix with LOD scores.")
public boolean CROSSCHECK_SAMPLES

CROSSCHECK_LIBRARIES

@Option(doc="Instead of producing the normal comparison of read-groups, roll fingerprints up to the library level and print out a library x library matrix with LOD scores.")
public boolean CROSSCHECK_LIBRARIES

NUM_THREADS

@Option(doc="The number of threads to use to process BAM files and generate Fingerprints.")
public int NUM_THREADS

ALLOW_DUPLICATE_READS

@Option(doc="Allow the use of duplicate reads in performing the comparison. Can be useful when duplicate marking has been overly aggressive and coverage is low.")
public boolean ALLOW_DUPLICATE_READS

GENOTYPING_ERROR_RATE

@Option(doc="Assumed genotyping error rate that provides a floor on the probability that a genotype comes from the expected sample.")
public double GENOTYPING_ERROR_RATE

OUTPUT_ERRORS_ONLY

@Option(doc="If true then only read groups that do not relate to each other as expected will have their LODs reported.")
public boolean OUTPUT_ERRORS_ONLY

LOSS_OF_HET_RATE

@Option(doc="The rate at which a het in a normal sample turns into a hom in the tumor.",
        optional=true)
public double LOSS_OF_HET_RATE

EXPECT_ALL_READ_GROUPS_TO_MATCH

@Option(doc="Expect all read groups\' fingerprints to match, irrespective of their sample names.  By default (with this value set to false), read groups with different sample names are expected to mismatch, and those with the same sample name are expected to match.")
public boolean EXPECT_ALL_READ_GROUPS_TO_MATCH

EXIT_CODE_WHEN_MISMATCH

@Option(doc="When one or more mismatches between read groups are detected, exit with this value instead of 0.")
public int EXIT_CODE_WHEN_MISMATCH

EXPECTED_MATCH

public static final java.lang.String EXPECTED_MATCH

See Also:

Constant Field Values

EXPECTED_MISMATCH

public static final java.lang.String EXPECTED_MISMATCH

See Also:

Constant Field Values

UNEXPECTED_MATCH

public static final java.lang.String UNEXPECTED_MATCH

See Also:

Constant Field Values

UNEXPECTED_MISMATCH

public static final java.lang.String UNEXPECTED_MISMATCH

See Also:

Constant Field Values

Constructor Detail

CrosscheckReadGroupFingerprints

public CrosscheckReadGroupFingerprints()

Method Detail

main

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

Stock main method.

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.