package vcf
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class
AssessPhasing
extends FgBioTool with LazyLogging
 Annotations
 @ClpAnnotation()

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
Metrics produced by
AssessPhasing
describing various statistics assessing the performance of phasing variants relative to a known set of phased variant calls.Metrics produced by
AssessPhasing
describing various statistics assessing the performance of phasing variants relative to a known set of phased variant calls. Included are methods for assessing sensitivity and accuracy from a number of previous papers (ex. http://dx.doi.org/10.1038%2Fng.3119).The N50, N90, and L50 statistics are defined as follows:  The N50 is the longest block length such that the bases covered by all blocks this length and longer are at least 50% of the # of bases covered by all blocks.  The N90 is the longest block length such that the bases covered by all blocks this length and longer are at least 90% of the # of bases covered by all blocks.  The L50 is the smallest number of blocks such that the sum of the lengths of the blocks is
>=
50% of the sum of the lengths of all blocks. 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
The fraction of switch sites without short switch errors (
1  (num_short_switch_errors / num_switch_sites)
). long_accuracy
The fraction of switch sites without long switch errors (
1  (num_long_switch_errors / num_switch_sites)
). illumina_point_accuracy
The fraction of switch sites without point switch errors according to the Illumina method defining switch sites and errors (
1  (num_illumina_point_switch_errors / num_illumina_switch_sites )
). illumina_long_accuracy
The fraction of switch sites wihtout long switch errors according to the Illumina method defining switch sites and errors (
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.
 sealed trait BlockInfo extends AnyRef

class
HapCutToVcf
extends FgBioTool with LazyLogging
 Annotations
 @ClpAnnotation()
 trait HeaderLines extends AnyRef

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.

class
MakeMixtureVcf
extends FgBioTool with LazyLogging
 Annotations
 @ClpAnnotation()

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()
 case class PhaseBlock extends GenomicSpan with Product with Serializable

case class
PhaseBlockLengthMetric
(dataset: String, length: Long = 0, count: Long = 0) extends Metric with Product with Serializable
Metrics produced by
AssessPhasing
describing the number of phased blocks of a given length.Metrics produced by
AssessPhasing
describing the number of phased blocks of a given length. The output will have multiple rows, one for each observed phased block length. dataset
The name of the dataset being assessed (i.e. "truth" or "called").
 length
The length of the phased block.
 count
The number of phased blocks of the given length.

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.
Value Members
 object AssessPhasing
 object AssessPhasingMetric extends Serializable
 object ByIntervalListVariantContextIterator
 object HapCut1VcfHeaderLines extends HeaderLines
 object HapCut2VcfHeaderLines extends HeaderLines
 object HapCutReader
 object HapCutType extends Enumeration
 object HeaderLines
 object JointVariantContextIterator
 object MakeMixtureVcf
 object MakeTwoSampleMixtureVcf
 object PhaseBlock extends LazyLogging with Serializable
 object PhaseBlockLengthMetric extends Serializable
 object VariantMask