Class AlleleBalanceFilter

java.lang.Object
picard.vcf.filter.AlleleBalanceFilter
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.
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final String
    The filter string used for sites that fail the allele balance filter.
  • Constructor Summary

    Constructors
    Constructor
    Description
    AlleleBalanceFilter(double hetAlleleBalance)
     
  • Method Summary

    Modifier and Type
    Method
    Description
    filter(htsjdk.variant.variantcontext.VariantContext ctx)
    Check to see if the VariantContext should have a filter applied to it.
    List<htsjdk.variant.vcf.VCFFilterHeaderLine>
    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 Details

    • AB_FILTER

      public static final String AB_FILTER
      The filter string used for sites that fail the allele balance filter.
      See Also:
  • Constructor Details

    • AlleleBalanceFilter

      public AlleleBalanceFilter(double hetAlleleBalance)
  • Method Details

    • 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 interface VariantFilter
    • 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 interface VariantFilter