picard.vcf.filter

Class GenotypeQualityFilter

java.lang.Object

picard.vcf.filter.GenotypeQualityFilter

All Implemented Interfaces:

GenotypeFilter

public class GenotypeQualityFilter
extends java.lang.Object
implements GenotypeFilter

Genotype filter that filters out genotypes below a given quality threshold.

Author:

tfennell

Constructor Summary

Constructors

Constructor and Description
GenotypeQualityFilter(int minGq)

Method Summary

Modifier and Type	Method and Description
java.lang.String	filter(htsjdk.variant.variantcontext.VariantContext ctx, htsjdk.variant.variantcontext.Genotype gt) Test whether or not the genotype should be filtered out.

Methods inherited from class java.lang.Object

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

Constructor Detail

GenotypeQualityFilter

public GenotypeQualityFilter(int minGq)

Method Detail

filter

public java.lang.String filter(htsjdk.variant.variantcontext.VariantContext ctx,
                               htsjdk.variant.variantcontext.Genotype gt)

Description copied from interface: GenotypeFilter

Test whether or not the genotype should be filtered out. If so return a filter string, otherwise return null.

Specified by:

filter in interface GenotypeFilter