org.molgenis.data.annotation.core.entity.impl.gavin

Class GavinAlgorithm

java.lang.Object

org.molgenis.data.annotation.core.entity.impl.gavin.GavinAlgorithm

public class GavinAlgorithm
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static int	EXTRA_SENSITIVITY_FACTOR Sensitivity is more important than specificity, so we can adjust this parameter to globally adjust the thresholds.
static int	GENOMEWIDE_CADD_THRESHOLD
static double	GENOMEWIDE_MAF_THRESHOLD
static String	NAME

Constructor Summary

Constructors

Constructor and Description
GavinAlgorithm()

Method Summary

Modifier and Type	Method and Description
Judgment	classifyVariant(Impact impact, Double caddScaled, Double exacMAF, String gene, GavinThresholds gavinThresholds) Classifies a variant using the given GavinThresholds.
Judgment	genomewideClassifyVariant(Impact impact, Double caddScaled, Double exacMAF, String gene) Classifies a variant based on genome-wide thresholds

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

NAME

public static final String NAME

See Also:

Constant Field Values

GENOMEWIDE_MAF_THRESHOLD

public static final double GENOMEWIDE_MAF_THRESHOLD

See Also:

Constant Field Values

GENOMEWIDE_CADD_THRESHOLD

public static final int GENOMEWIDE_CADD_THRESHOLD

See Also:

Constant Field Values

EXTRA_SENSITIVITY_FACTOR

public static final int EXTRA_SENSITIVITY_FACTOR

Sensitivity is more important than specificity, so we can adjust this parameter to globally adjust the thresholds.

• At a setting of 1, ie. default behaviour, GAVIN is 89% sensitive and 83% specific
• at a setting of 5, a more sensitive setting, GAVIN is 92% sensitive and 78% specific

Technically we lose more than we gain, but having >90% sensitivity is really important. Better to have a few more false positives than to miss a true positive.

See Also:

Constant Field Values

Constructor Detail

GavinAlgorithm

public GavinAlgorithm()

Method Detail

classifyVariant

public Judgment classifyVariant(Impact impact,
                                Double caddScaled,
                                Double exacMAF,
                                String gene,
                                GavinThresholds gavinThresholds)

Classifies a variant using the given GavinThresholds.

Parameters:

impact - putative impact of the variant, determined by snpEff

caddScaled - scaled cadd score for the variant

exacMAF - maf of the variant, determined by exac

gene - gene of the variant

gavinThresholds - the GavinThresholds for this gene

Returns:

the Judgment of the gavin algorithm

genomewideClassifyVariant

public Judgment genomewideClassifyVariant(Impact impact,
                                          Double caddScaled,
                                          Double exacMAF,
                                          String gene)

Classifies a variant based on genome-wide thresholds

Parameters:

impact - putative impact of the variant, determined by snpEff

caddScaled - scaled cadd score for the variant

exacMAF - maf of the variant, determined by exac

gene - gene of the variant

Returns:

the Judgment of the gavin algorithm