Class 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 Detail

      • 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
    • Constructor Detail

      • AlleleBalanceFilter

        public AlleleBalanceFilter​(double hetAlleleBalance)
    • Method Detail

      • 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