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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Average Coverage, Sample Level, Pool A Targets

Detailed view of coverage values for each sample, grouped by UMI family type

PreviousDistribution of ACCESS panel A coverage valuesNextUMI Family types Composition (Pool A)

Last updated 4 years ago

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Theoretical Method

Calculate average coverage of each of four possible bam types for each sample:

  • Standard or “Uncollapsed”

  • Collapsed unfiltered: after merging all reads from same UMI family

  • Collapsed simplex: three or more reads found on one strand

  • Collapsed duplex: one or more reads found on both strands (top and bottom)

Coverage is first averaged across each position in a single bait region. Then, the average across each bait region in the sample represents the sample’s final coverage value.

Technical Methods

  • Tool Used:

    • Marianas

    • Waltz CountReads

    • aggregate_bam_metrics.sh

    • tables_module.py

    • plots_module.r

  • Input

    • 4 bams per sample (Standard, U, S, D)

  • Output

    • sample_id-intervals.txt (sample level, included for all 4 bam types)

    • waltz-coverage.txt (aggregated across samples, for a single bam type)

    • coverage_agg.txt (aggregated across all samples, all bam types, pools A / B)

Interpretations

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