Package picard.vcf.filter

Class QdFilter

java.lang.Object
picard.vcf.filter.QdFilter
All Implemented Interfaces:
VariantFilter
public class QdFilter extends Object implements VariantFilter
Filters out sites that have a QD annotation applied to them and where the QD value is lower than a lower limit.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final String
    FILTER_NAME
     

  • Constructor Summary

    Constructors
    Constructor
    Description
    QdFilter(double minimumQd)
     

  • Method Summary

    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.

    Methods inherited from class java.lang.Object

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

  • Field Details

  • Constructor Details

    • QdFilter

      public QdFilter(double minimumQd)

  • Method Details

    • 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

    • 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