Type Members

1.  class AssessPhasing extends FgBioTool with LazyLogging

   Annotations

   @ClpAnnotation()

2.  case class AssessPhasingMetric (num_called: Long = 0, num_phased: Long = 0, num_truth: Long = 0, num_truth_phased: Long = 0, num_called_with_truth_phased: Long = 0, num_phased_with_truth_phased: Long = 0, num_truth_phased_in_called_block: Long = 0, num_both_phased_in_called_block: Long = 0, num_short_switch_errors: Long = 0, num_long_switch_errors: Long = 0, num_switch_sites: Long = 0, num_illumina_point_switch_errors: Long = 0, num_illumina_long_switch_errors: Long = 0, num_illumina_switch_sites: Long = 0, frac_phased: Double = 0, frac_phased_with_truth_phased: Double = 0, frac_truth_phased_in_called_block: Double = 0, frac_phased_with_truth_phased_in_called_block: Double = 0, short_accuracy: Double = 0, long_accuracy: Double = 0, illumina_point_accuracy: Double = 0, illumina_long_accuracy: Double = 0, mean_called_block_length: Double = 0, median_called_block_length: Double = 0, stddev_called_block_length: Double = 0, n50_called_block_length: Double = 0, n90_called_block_length: Double = 0, l50_called: Double = 0, mean_truth_block_length: Double = 0, median_truth_block_length: Double = 0, stddev_truth_block_length: Double = 0, n50_truth_block_length: Double = 0, n90_truth_block_length: Double = 0, l50_truth: Double = 0) extends Metric with Product with Serializable

   Some counts about phasing

   Some counts about phasing

   num_called

   the number of variants called.

   num_phased

   the number of variants called with phase.

   num_truth

   the number of variants with known truth genotypes.

   num_truth_phased

   the number of variants with known truth genotypes with phase.

   num_called_with_truth_phased

   the number of variants called that had a known phased genotype.

   num_phased_with_truth_phased

   the number of variants called with phase that had a known phased genotype.

   num_truth_phased_in_called_block

   the number of known phased variants that were in a called phased block.

   num_both_phased_in_called_block

   the number of called phase variants that had a known phased genotype in a called phased block.

   num_short_switch_errors

   the number of short switch errors (isolated switch errors).

   num_long_switch_errors

   the number of long switch errors (# of runs of consecutive switch errors).

   num_switch_sites

   the number of sites that could be (short or long) switch errors (i.e. the # of sites with both known and called phased variants).

   num_illumina_point_switch_errors

   the number of point switch errors (defined in http://dx.doi.org/10.1038%2Fng.3119).

   num_illumina_long_switch_errors

   the number of long switch errors (defined in http://dx.doi.org/10.1038%2Fng.3119).

   num_illumina_switch_sites

   the number of sites that could be (point or long) switch errors (defined in http://dx.doi.org/10.1038%2Fng.3119).

   frac_phased

   the fraction of called variants with phase.

   frac_phased_with_truth_phased

   the fraction of known phased variants called with phase.

   frac_truth_phased_in_called_block

   the fraction of phased known genotypes in a called phased block.

   frac_phased_with_truth_phased_in_called_block

   the fraction of called phased variants that had a known phased genotype in a called phased block.

   short_accuracy

   1 - (num_short_switch_errors / num_switch_sites)

   long_accuracy

   1 - (num_long_switch_errors / num_switch_sites)

   illumina_point_accuracy

   1 - (num_illumina_point_switch_errors / num_illumina_switch_sites )

   illumina_long_accuracy

   1 - (num_illumina_long_switch_errors / num_illumina_switch_sites )

   mean_called_block_length

   the mean phased block length in the callset.

   median_called_block_length

   the median phased block length in the callset.

   stddev_called_block_length

   the standard deviation of the phased block length in the callset.

   n50_called_block_length

   the N50 of the phased block length in the callset.

   n90_called_block_length

   the N90 of the phased block length in the callset.

   l50_called

   the L50 of the phased block length in the callset.

   mean_truth_block_length

   the mean phased block length in the truth.

   median_truth_block_length

   the median phased block length in the truth.

   stddev_truth_block_length

   the standard deviation of the phased block length in the truth.

   n50_truth_block_length

   the N50 of the phased block length in the truth.

   n90_truth_block_length

   the N90 of the phased block length in the callset.

   l50_truth

   the L50 of the phased block length in the callset.

3.  sealed trait BlockInfo extends AnyRef
4.  class HapCutToVcf extends FgBioTool with LazyLogging

   Annotations

   @ClpAnnotation()

5.  trait HeaderLines extends AnyRef
6.  class JointVariantContextIterator extends Iterator[Seq[Option[VariantContext]]]

   Iterates over multiple variant context iterators such that we return a list of contexts for the union of sites across the iterators.

   Iterates over multiple variant context iterators such that we return a list of contexts for the union of sites across the iterators. If samples is given, we subset each variant context to just that sample.

7.  class MakeMixtureVcf extends FgBioTool with LazyLogging

   Annotations

   @ClpAnnotation()

8.  class MakeTwoSampleMixtureVcf extends FgBioTool

   Creates a VCF by mixing two germline samples at a given proportion.

   Creates a VCF by mixing two germline samples at a given proportion.

   Annotations

   @ClpAnnotation()

9.  case class PhaseBlock extends GenomicSpan with Product with Serializable
10.  case class PhaseBlockLengthMetric (dataset: String, length: Long = 0, count: Long = 0) extends Metric with Product with Serializable

    Provides the number of phased blocks of a given length.

    Provides the number of phased blocks of a given length.

    dataset

    the name of the dataset (ex. truth or call)

    length

    the length of the phased block

    count

    the number of phased blocks of the given length.

11.  class VariantMask extends AnyRef

    Simple mask that loads variants one reference sequence at a time and creates a compact representation allowing for rapid querying of whether or not positions are overlapped by one or more variants.