Field Detail

• INPUT

  @Argument(shortName="I",
            doc="One or more input files (or lists of files) with which to compare fingerprints.",
            minElements=1)
  public List<String> INPUT

• INPUT_SAMPLE_MAP

  @Argument(doc="A tsv with two columns representing the sample as it appears in the INPUT data (in column 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second column). Need only include the samples that change. Values in column 1 should be unique. Values in column 2 should be unique even in union with the remaining unmapped samples. Should only be used with SECOND_INPUT. ",
            optional=true)
  public File INPUT_SAMPLE_MAP

• SECOND_INPUT

  @Argument(shortName="SI",
            optional=true,
            mutex="MATRIX_OUTPUT",
            doc="A second set of input files (or lists of files) with which to compare fingerprints. If this option is provided the tool compares each sample in INPUT with the sample from SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool will proceed to check the matching samples, but report the missing samples and return a non-zero error-code.")
  public List<String> SECOND_INPUT

• SECOND_INPUT_SAMPLE_MAP

  @Argument(doc="A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in column 1) and the sample as it should be used for comparisons to INPUT (in the second column). Need only include the samples that change. Values in column 1 should be unique. Values in column 2 should be unique even in union with the remaining unmapped samples. Should only be used with SECOND_INPUT. ",
            optional=true)
  public File SECOND_INPUT_SAMPLE_MAP

• CROSSCHECK_MODE

  @Argument(doc="An argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur. ")
  public picard.fingerprint.CrosscheckFingerprints.CrosscheckMode CROSSCHECK_MODE

• OUTPUT

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

• MATRIX_OUTPUT

  @Argument(shortName="MO",
            optional=true,
            doc="Optional output file to write matrix of LOD scores to. This is less informative than the metrics output and only contains Normal-Normal LOD score (i.e. doesn\'t account for Loss of Heterozygosity). It is however sometimes easier to use visually.",
            mutex="SECOND_INPUT")
  public File MATRIX_OUTPUT

• HAPLOTYPE_MAP

  @Argument(shortName="H",
            doc="The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.")
  public File HAPLOTYPE_MAP

• LOD_THRESHOLD

  @Argument(shortName="LOD",
            doc="If any two groups (with the same sample name) match with a LOD score lower than the threshold the tool will exit with a non-zero code to indicate error. Program will also exit with an error if it finds two groups with different sample name that match with a LOD score greater than -LOD_THRESHOLD.\n\nLOD score 0 means equal likelihood that the groups match vs. come from different individuals, negative LOD score -N, mean 10^N time more likely that the groups are from different individuals, and +N means 10^N times more likely that the groups are from the same individual. ")
  public double LOD_THRESHOLD

• CROSSCHECK_BY

  @Argument(doc="Specificies which data-type should be used as the basic comparison unit. Fingerprints from readgroups can be \"rolled-up\" to the LIBRARY, SAMPLE, or FILE level before being compared. Fingerprints from VCF can be be compared by SAMPLE or FILE.")
  public CrosscheckMetric.DataType CROSSCHECK_BY

• NUM_THREADS

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

• CALCULATE_TUMOR_AWARE_RESULTS

  @Argument(doc="specifies whether the Tumor-aware result should be calculated. These are time consuming and can roughly double the runtime of the tool. When crosschecking many groups not calculating the tumor-aware  results can result in a significant speedup.")
  public boolean CALCULATE_TUMOR_AWARE_RESULTS

• ALLOW_DUPLICATE_READS

  @Argument(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

  @Argument(doc="Assumed genotyping error rate that provides a floor on the probability that a genotype comes from the expected sample. Must be greater than zero. ")
  public double GENOTYPING_ERROR_RATE

• OUTPUT_ERRORS_ONLY

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

• LOSS_OF_HET_RATE

  @Argument(doc="The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via loss of heterozygosity) in the tumor (model assumes independent events, so this needs to be larger than reality).",
            optional=true)
  public double LOSS_OF_HET_RATE

• EXPECT_ALL_GROUPS_TO_MATCH

  @Argument(doc="Expect all groups\' fingerprints to match, irrespective of their sample names.  By default (with this value set to false), groups (readgroups, libraries, files, or samples) with different sample names are expected to mismatch, and those with the same sample name are expected to match. ")
  public boolean EXPECT_ALL_GROUPS_TO_MATCH

• EXIT_CODE_WHEN_MISMATCH

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

Constructor Detail

• CrosscheckFingerprints

  public CrosscheckFingerprints()

Method Detail

• customCommandLineValidation

  protected 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.

• getFingerprintIdDetailsStringFunction

  public static Function<FingerprintIdDetails,String> getFingerprintIdDetailsStringFunction​(CrosscheckMetric.DataType CROSSCHECK_BY)

• mergeFingerprintsBy

  public static Map<FingerprintIdDetails,Fingerprint> mergeFingerprintsBy​(Map<FingerprintIdDetails,Fingerprint> fingerprints,
                                                                          Function<FingerprintIdDetails,String> by)