Access Quality Control (v1)
  • Introduction
  • Meta information per sample
  • Raw read-pair counts (standard BAM)
  • On Target Coverage
  • Fraction of reads mapping to the human genome
  • “On Bait” reads localized to ACCESS panel
  • Coverage vs GC content
  • Insert Size Distribution
  • Distribution of ACCESS panel A coverage values
  • Average Coverage, Sample Level, Pool A Targets
  • UMI Family types Composition (Pool A)
  • Average Coverage, Sample Level, Pool B Targets
  • UMI Family types Composition (Pool B)
  • Base Quality Recalibration Scores
  • UMI family sizes (Simplex reads)
  • UMI family sizes (Duplex reads)
  • Sample Level Noise
  • Noise by Substitution Type
  • Contributing Sites for Noise
  • Hotspots In Normals
  • Sample mix-up
  • (Un)expected (Mis)matches Tables
  • Major Contamination
  • Minor Contamination
  • Duplex Minor Contamination
  • Sex Mismatch
  • FAQ
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Meta information per sample

Overview of library and coverage information for the current set of samples run through ACCESS assay

PreviousIntroductionNextRaw read-pair counts (standard BAM)

Last updated 4 years ago

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Technical Method

  • Tool Used: plots_module.r

  • Input:

    • title_file.txt

    • coverage_agg.txt

    • average_coverage_across_exon_targets_duplex_A.txt

  • Output: N/A

Interpretation

  • Library input should be ~5-20ng for ctDNA, ~200ng for buffy coats (or the maximum amount available if these thresholds can’t be met)

  • Capture input should be ~500ng or maximum available after library generation

  • Expected range of coverage values:

      • Raw coverage A panel:

        • ctDNA: ~ 15000x-20000x

        • Buffy Coat: ~ 500x-1000x

      • Raw coverage B panel:

        • ctDNA: ~ 1000x-1,500x

        • Buffy Coat: ~ 500x-1000x

      • Duplex coverage A panel:

        • ctDNA: ~ 500x-2000x

        • Buffy Coat: ~ 10x-50x

Note: Samples that don’t meet the library input criteria will have lower coverage