Package picard.vcf

Class CollectVariantCallingMetrics.VariantCallingDetailMetrics

    • Field Detail

      • SAMPLE_ALIAS

        public String SAMPLE_ALIAS
        The name of the sample being assayed
      • HET_HOMVAR_RATIO

        public double HET_HOMVAR_RATIO
        (count of hets)/(count of homozygous non-ref) for this sample
      • PCT_GQ0_VARIANTS

        public double PCT_GQ0_VARIANTS
        The percentage of variants in a particular sample that have a GQ score of 0.
      • TOTAL_GQ0_VARIANTS

        public long TOTAL_GQ0_VARIANTS
        The total number of variants in a particular sample that have a GQ score of 0.
      • TOTAL_HET_DEPTH

        public long TOTAL_HET_DEPTH
        total number of reads (from AD field) for passing bi-allelic SNP hets for this sample
    • Constructor Detail

      • VariantCallingDetailMetrics

        public VariantCallingDetailMetrics()
    • Method Detail

      • getFileExtension

        public static String getFileExtension()
      • calculateFromDerivedFields

        public void calculateFromDerivedFields()