picard.vcf.filter

Class AlleleBalanceFilter

java.lang.Object

picard.vcf.filter.AlleleBalanceFilter

All Implemented Interfaces:

VariantFilter

public class AlleleBalanceFilter
extends java.lang.Object
implements VariantFilter

Filters out a record if the allele balance for heterozygotes is out of a defined range across all samples. The threshold is set as the minimum fraction of the data drawn from the less-represented allele - e.g. 0.3 would set that whichever allele has lower representation across all heterozygous individuals must account for at least 30% of the total observations.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	AB_FILTER The filter string used for sites that fail the allele balance filter.

Constructor Summary

Constructors

Constructor and Description
AlleleBalanceFilter(double hetAlleleBalance)

Method Summary

Modifier and Type	Method and Description
java.lang.String	filter(htsjdk.variant.variantcontext.VariantContext ctx) Check to see if the VariantContext should have a filter applied to it.
java.util.List<htsjdk.variant.vcf.VCFFilterHeaderLine>	headerLines() Return VCF header lines that define filters that may be applied by the VariantFilter.

Methods inherited from class java.lang.Object

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

Field Detail

AB_FILTER

public static final java.lang.String AB_FILTER

The filter string used for sites that fail the allele balance filter.

See Also:

Constant Field Values

Constructor Detail

AlleleBalanceFilter

public AlleleBalanceFilter(double hetAlleleBalance)

Method Detail

headerLines

public java.util.List<htsjdk.variant.vcf.VCFFilterHeaderLine> headerLines()

Description copied from interface: VariantFilter

Return VCF header lines that define filters that may be applied by the VariantFilter.

Specified by:

headerLines in interface VariantFilter

filter

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

Description copied from interface: VariantFilter

Check to see if the VariantContext should have a filter applied to it. If so return the filter string, otherwise return null.

Specified by:

filter in interface VariantFilter