Package picard.arrays

Class CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics

    • Field Detail

      • CHIP_WELL_BARCODE

        public String CHIP_WELL_BARCODE
        The chip well barcode of the Illumina array being assayed
      • SAMPLE_ALIAS

        public String SAMPLE_ALIAS
        The name of the sample
      • ANALYSIS_VERSION

        public Integer ANALYSIS_VERSION
        The version number of the analysis run
      • CHIP_TYPE

        public String CHIP_TYPE
        The chip type name
      • AUTOCALL_PF

        public Boolean AUTOCALL_PF
        Whether the sample passes QC based on call rate threshold
      • AUTOCALL_DATE

        public htsjdk.samtools.util.Iso8601Date AUTOCALL_DATE
        The date this sample was autocalled
      • IMAGING_DATE

        public htsjdk.samtools.util.Iso8601Date IMAGING_DATE
        The date that this sample was imaged
      • IS_ZCALLED

        public Boolean IS_ZCALLED
        Whether the sample was zcalled
      • AUTOCALL_GENDER

        public String AUTOCALL_GENDER
        The sex, as determined by Autocall
      • FP_GENDER

        public String FP_GENDER
        The sex, as reported for the fingerprinted sample
      • REPORTED_GENDER

        public String REPORTED_GENDER
        The sex, as reported by the collaborator
      • GENDER_CONCORDANCE_PF

        public Boolean GENDER_CONCORDANCE_PF
        Whether or not the three sexs agree
      • HET_PCT

        public double HET_PCT
        100 * (count of hets) / (total calls) for this sample
      • CLUSTER_FILE_NAME

        public String CLUSTER_FILE_NAME
        The name of the cluster file used
      • P95_GREEN

        public Integer P95_GREEN
        The 95th Intensity Percentile for the green color channel for this sample
      • P95_RED

        public Integer P95_RED
        The 95th Intensity Percentile for the red color channel for this sample
      • AUTOCALL_VERSION

        public String AUTOCALL_VERSION
        The version of autocall used for calling this sample
      • ZCALL_VERSION

        public String ZCALL_VERSION
        The version of ZCall used for calling this sample
      • EXTENDED_MANIFEST_VERSION

        public String EXTENDED_MANIFEST_VERSION
        The version of the Extended Illumina Manifest used for calling this sample
      • HET_HOMVAR_RATIO

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

        public String SCANNER_NAME
        The name of the scanner used for this sample
    • Constructor Detail

      • ArraysVariantCallingDetailMetrics

        public ArraysVariantCallingDetailMetrics()