Nucleo Quality Control
  • 🌸Nucleo Quality Control
    • Workflow description
    • Requirements
    • Installation and Usage
    • Workflow inputs
      • Input for nucleo_qc.cwl
      • Input for nucleo_aggregate_visualize.cwl
    • Workflow outputs
    • ☀️Interpretation - MultiQC
      • Summary QC metrics
      • Coverage vs GC content
      • Capture Metrics
      • Insert Size
      • Target coverage distribution
      • Duplex Metrics
        • Duplex family sizes
        • Simplex family sizes
        • Duplex yield metrics
      • Mean Base Quality
      • Duplex Noise Metrics
      • Contamination
        • Hotspot in Normals
        • Major contamination
        • Minor contamination
        • Contributing sites
      • Fingerprinting
      • QC thresholds
  • 🇬🇷Interpretation - Athena Coverage report
    • Installation and running
    • Interpretation coverage report
      • Report details
      • Summary
      • Exons with <100% coverage at 500x
      • Per gene coverage summary
      • Per exon coverage
      • Coverage of Known Variants
      • Coverage per chromosome
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  1. Interpretation - Athena Coverage report

Installation and running

The athena tool is made of 3 parts; 1) annotate the bed file 2) generate statistic files 3) generate the coverage report. This can be run independently or together with a single workflow:

Run independently:

  1. Annotate each region of the bed file with the gene, exon and per base coverage data using https://github.com/msk-access/cwl-commandlinetools/blob/develop/athena/1.4.2/annotate_bed/annotate_bed.cwl

  2. Generate per exon and per gene statistics using https://github.com/msk-access/cwl-commandlinetools/blob/develop/athena/1.4.2/coverage_stats_single/coverage_stats_single.cwl

  3. Generate HTML coverage report with https://github.com/msk-access/cwl-commandlinetools/tree/develop/athena/1.4.2/coverage_report_single

Run three steps with a single workflow:

  • Run all 3 steps above using a single workflow using https://github.com/msk-access/cwl_subworkflows/blob/develop/athena_report/athena_report.cwl

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Last updated 2 years ago

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