Thursday, 22 December 2011

Picard Metrics Definitions - USEFUL!
  1. AlignmentSummaryMetrics: High level metrics about the alignment of reads within a SAM file, produced by the CollectAlignmentSummaryMetrics program and usually stored in a file with the extension ".alignment_summary_metrics".
  2. DuplicationMetrics: Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords.
  3. ExtractIlluminaBarcodes.BarcodeMetric: Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in the basecalls directory and determine to which barcode each read should be assigned.
  4. GcBiasDetailMetrics: Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.
  5. GcBiasSummaryMetrics: High level metrics that capture how biased the coverage in a certain lane is.
  6. HsMetrics: The set of metrics captured that are specific to a hybrid selection analysis.
  7. InsertSizeMetrics: Metrics about the insert size distribution of a paired-end library, created by the CollectInsertSizeMetrics program and usually written to a file with the extension ".insert_size_metrics".
  8. MultilevelMetrics:
  9. RnaSeqMetrics: Metrics about the alignment of RNA-seq reads within a SAM file to genes, produced by the CollectRnaSeqMetrics program and usually stored in a file with the extension ".rna_metrics".
  10. SamFileValidator.ValidationMetrics:

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