Package picard.arrays

Class CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics

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

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

    • 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 Details

    • ArraysVariantCallingSummaryMetrics

      public ArraysVariantCallingSummaryMetrics()
  • Method Details