Package picard.vcf

Class CollectVariantCallingMetrics.VariantCallingSummaryMetrics

    • Field Detail

      • TOTAL_SNPS

        public long TOTAL_SNPS
        The number of passing bi-allelic SNPs calls (i.e. non-reference genotypes) that were examined
      • NUM_IN_DB_SNP

        public long NUM_IN_DB_SNP
        The number of passing bi-allelic SNPs found in dbSNP
      • NOVEL_SNPS

        public long NOVEL_SNPS
        The number of passing bi-allelic SNPS called that were not found in dbSNP
      • FILTERED_SNPS

        public long FILTERED_SNPS
        The number of SNPs that are filtered
      • PCT_DBSNP

        public float PCT_DBSNP
        The fraction of passing bi-allelic SNPs in dbSNP
      • DBSNP_TITV

        public double DBSNP_TITV
        The Transition/Transversion ratio of the passing bi-allelic SNP calls made at dbSNP sites
      • NOVEL_TITV

        public double NOVEL_TITV
        The Transition/Transversion ratio of the passing bi-allelic SNP calls made at non-dbSNP sites
      • TOTAL_INDELS

        public long TOTAL_INDELS
        The number of passing indel calls that were examined
      • NOVEL_INDELS

        public long NOVEL_INDELS
        The number of passing indels called that were not found in dbSNP
      • FILTERED_INDELS

        public long FILTERED_INDELS
        The number of indels that are filtered
      • PCT_DBSNP_INDELS

        public float PCT_DBSNP_INDELS
        The fraction of passing indels in dbSNP
      • NUM_IN_DB_SNP_INDELS

        public long NUM_IN_DB_SNP_INDELS
        The number of passing indels found in dbSNP
      • DBSNP_INS_DEL_RATIO

        public double DBSNP_INS_DEL_RATIO
        The Insertion/Deletion ratio of the indel calls made at dbSNP sites
      • NOVEL_INS_DEL_RATIO

        public double NOVEL_INS_DEL_RATIO
        The Insertion/Deletion ratio of the indel calls made at non-dbSNP sites
      • TOTAL_MULTIALLELIC_SNPS

        public double TOTAL_MULTIALLELIC_SNPS
        The number of passing multi-allelic SNP calls that were examined
      • NUM_IN_DB_SNP_MULTIALLELIC

        public double NUM_IN_DB_SNP_MULTIALLELIC
        The number of passing multi-allelic SNPs found in dbSNP
      • TOTAL_COMPLEX_INDELS

        public double TOTAL_COMPLEX_INDELS
        The number of passing complex indel calls that were examined
      • NUM_IN_DB_SNP_COMPLEX_INDELS

        public double NUM_IN_DB_SNP_COMPLEX_INDELS
        The number of passing complex indels found in dbSNP
      • SNP_REFERENCE_BIAS

        public double SNP_REFERENCE_BIAS
        The rate at which reference bases are observed at ref/alt heterozygous SNP sites.
      • NUM_SINGLETONS

        public long NUM_SINGLETONS
        For summary metrics, the number of variants that appear in only one sample. For detail metrics, the number of variants that appear only in the current sample.
    • Constructor Detail

      • VariantCallingSummaryMetrics

        public VariantCallingSummaryMetrics()
    • Method Detail

      • getFileExtension

        public static String getFileExtension()
      • calculateDerivedFields

        public void calculateDerivedFields()
        Description copied from class: MergeableMetricBase
        Placeholder method that will calculate the derived fields from the other ones. Classes that are derived from non-trivial derived classes should consider calling super.calculateDerivedFields() as well. Fields whose value will change due to this method should be annotated with NoMergingKeepsValue.
        Overrides:
        calculateDerivedFields in class MergeableMetricBase
      • calculateFromDerivedFields

        public void calculateFromDerivedFields​(long totalHetDepth)