Package picard.vcf.filter
Class AlleleBalanceFilter
- java.lang.Object
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- picard.vcf.filter.AlleleBalanceFilter
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- All Implemented Interfaces:
VariantFilter
public class AlleleBalanceFilter extends 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.
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Constructor Summary
Constructors Constructor Description AlleleBalanceFilter(double hetAlleleBalance)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description String
filter(htsjdk.variant.variantcontext.VariantContext ctx)
Check to see if the VariantContext should have a filter applied to it.List<htsjdk.variant.vcf.VCFFilterHeaderLine>
headerLines()
Return VCF header lines that define filters that may be applied by the VariantFilter.
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Field Detail
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AB_FILTER
public static final String AB_FILTER
The filter string used for sites that fail the allele balance filter.- See Also:
- Constant Field Values
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Method Detail
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headerLines
public 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 interfaceVariantFilter
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filter
public 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 interfaceVariantFilter
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