package vcf
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Type Members
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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
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class
HapCutToVcf
extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
- trait HeaderLines extends AnyRef
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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.
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class
MakeMixtureVcf
extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
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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
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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.
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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