NGS Data QC

Implementation of the ngs_data_qc step

Default Configuration

The default configuration is as follows.

# Default configuration ngs_mapping
step_config:
  ngs_data_qc:
    path_link_in: ""  # OPTIONAL Override data set configuration search paths for FASTQ files
    tools: [fastqc, picard]  # REQUIRED - available: 'fastqc' & 'picard' (for QC on bam files)
    picard:
      path_ngs_mapping: ../ngs_mapping  # REQUIRED
      path_to_baits: ""                 # Required when CollectHsMetrics is among the programs
      path_to_targets: ""               # When missing, same as baits
      bait_name: ""                     # Exon enrichment kit name (optional)
      programs: []  # Available metrics:
                    # * Generic metrics [* grouped into CollectMultipleMetrics]
      #                 - CollectAlignmentSummaryMetrics      *
      #                 - CollectBaseDistributionByCycle      *
      #                 - CollectGcBiasMetrics                *
      #                 - CollectInsertSizeMetrics            *
      #                 - CollectJumpingLibraryMetrics
      #                 - CollectOxoGMetrics
      #                 - CollectQualityYieldMetrics          *
      #                 - CollectSequencingArtifactMetrics    *
      #                 - EstimateLibraryComplexity
      #                 - MeanQualityByCycle                  *
      #                 - QualityScoreDistribution            *
                    # * WGS-specific metrics
      #                 - CollectRawWgsMetrics
      #                 - CollectWgsMetrics
      #                 - CollectWgsMetricsWithNonZeroCoverage
                    # * Other assay-specific metrics
      #                 - CollectHsMetrics                    Whole Exome Sequencing
      #                 - CollectTargetedPcrMetrics           Panel sequencing
      #                 - CollectRnaSeqMetrics                mRNA sequencing, not implemented yet
      #                 - CollectRbsMetrics                   bi-sulfite sequencing, not implemented yet