Package picard.arrays

Class CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics

    • Field Detail

      • NUM_ASSAYS

        public long NUM_ASSAYS
        The total number of assays (SNP and indels) in the VCF
      • NUM_NON_FILTERED_ASSAYS

        public long NUM_NON_FILTERED_ASSAYS
        The total number of NON-filtered assays in the VCF
      • NUM_FILTERED_ASSAYS

        public long NUM_FILTERED_ASSAYS
        The total number of filtered assays in the VCF
      • NUM_ZEROED_OUT_ASSAYS

        public long NUM_ZEROED_OUT_ASSAYS
        The total number of zeroed-out (filtered out by Illumina in chip design) assays in the VCF
      • NUM_SNPS

        public long NUM_SNPS
        The number of bi-allelic SNP calls
      • NUM_INDELS

        public long NUM_INDELS
        The number of indel calls
      • NUM_CALLS

        public long NUM_CALLS
        The number of passing calls
      • NUM_AUTOCALL_CALLS

        public long NUM_AUTOCALL_CALLS
        The number of passing autocall calls
      • NUM_NO_CALLS

        public long NUM_NO_CALLS
        The number of no-calls
      • NUM_IN_DB_SNP

        public long NUM_IN_DB_SNP
        The number of high confidence SNPs found in dbSNP
      • NOVEL_SNPS

        public long NOVEL_SNPS
        The number of high confidence SNPS called that were not found in dbSNP
      • PCT_DBSNP

        public float PCT_DBSNP
        The fraction of high confidence SNPs in dbSNP
      • CALL_RATE

        public float CALL_RATE
        The overall call rate
      • AUTOCALL_CALL_RATE

        public float AUTOCALL_CALL_RATE
        The overall autocall call rate
      • 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

      • ArraysVariantCallingSummaryMetrics

        public ArraysVariantCallingSummaryMetrics()