picard.vcf.filter

Class DepthFilter

java.lang.Object

picard.vcf.filter.DepthFilter

All Implemented Interfaces:

GenotypeFilter

public class DepthFilter
extends java.lang.Object
implements GenotypeFilter

Filters out a record if all variant samples have depth lower than the given value.

Constructor Summary

Constructors

Constructor and Description
DepthFilter(int minDepth)

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

DepthFilter

public DepthFilter(int minDepth)

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