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 B Targets

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

PreviousUMI Family types Composition (Pool A)NextUMI Family types Composition (Pool B)

Last updated 4 years ago

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Theoretical Method

Similarly to the Pool A Targets, coverage is calculated for each UMI family type, over the Pool B genomic bait regions. These coverage values are lower for cfDNA samples (which use a 50:1 pool ratio) but should be comparable for buffy coat samples (which use a 1:1 pool ratio).

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 Aim is to have high coverage, and as much duplex “saturation” as possible. See title page for specific pass / fail criteria.