Field Detail

• INPUT

  @Argument(shortName="I",
            doc="Input VCF or BCF with genotypes.")
  public File INPUT

• TRIOS

  @Argument(shortName="PED",
            doc="File of Trio information in PED format (with no genotype columns).")
  public File TRIOS

• OUTPUT

  @Argument(shortName="O",
            doc="Output metrics file.")
  public File OUTPUT

• MIN_GQ

  @Argument(shortName="GQ",
            doc="Minimum genotyping quality (or non-ref likelihood) to perform tests.")
  public int MIN_GQ

• MIN_DP

  @Argument(shortName="DP",
            doc="Minimum depth in each sample to consider possible mendelian violations.")
  public int MIN_DP

• MIN_HET_FRACTION

  @Argument(shortName="MINHET",
            doc="Minimum allele balance at sites that are heterozygous in the offspring.")
  public double MIN_HET_FRACTION

• VCF_DIR

  @Argument(optional=true,
            doc="If provided, output per-family VCFs of mendelian violations into this directory.")
  public File VCF_DIR

• SKIP_CHROMS

  @Argument(doc="List of chromosome names to skip entirely.")
  public Set<String> SKIP_CHROMS

• MALE_CHROMS

  @Argument(doc="List of possible names for male sex chromosome(s)")
  public Set<String> MALE_CHROMS

• FEMALE_CHROMS

  @Argument(doc="List of possible names for female sex chromosome(s)")
  public Set<String> FEMALE_CHROMS

• PSEUDO_AUTOSOMAL_REGIONS

  @Argument(doc="List of chr:start-end for pseudo-autosomal regions on the female sex chromosome. Defaults to HG19/b37 & HG38 coordinates.")
  public Set<String> PSEUDO_AUTOSOMAL_REGIONS

• THREAD_COUNT

  @Argument(doc="The number of threads that will be used to collect the metrics. ")
  public int THREAD_COUNT

• TAB_MODE

  @Argument(doc="If true then fields need to be delimited by a single tab. If false the delimiter is one or more whitespace characters. Note that tab mode does not strictly follow the PED spec")
  public boolean TAB_MODE

Constructor Detail

• FindMendelianViolations

  public FindMendelianViolations()

Method Detail

• customCommandLineValidation

  protected String[] customCommandLineValidation()

  Validates that the sex chromosomes don't overlap and parses the pseudo-autosomal regions into usable objects to ensure their parsability

  Overrides:

  customCommandLineValidation in class CommandLineProgram

  Returns:

• 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.