Package picard.arrays

Class CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
Enclosing class:
CollectArraysVariantCallingMetrics

@DocumentedFeature(groupName="Metrics", summary="Metrics") public static class CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics extends CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
  • Field Details

    • 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
    • GTC_CALL_RATE

      public Double GTC_CALL_RATE
      The call rate as determined by Autocall/IAAP (and stored in the GTC File)
    • 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
    • PIPELINE_VERSION

      public String PIPELINE_VERSION
      The version of the pipeline used for this sample
  • Constructor Details

    • ArraysVariantCallingDetailMetrics

      public ArraysVariantCallingDetailMetrics()
  • Method Details