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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Distribution of ACCESS panel A coverage values

Ensure consistent coverage across ACCESS bait (or “probe”) regions

PreviousInsert Size DistributionNextAverage Coverage, Sample Level, Pool A Targets

Last updated 4 years ago

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Theoretical Method

Coverage of each genomic region in the ACCESS panel is grouped on a per-sample basis, and a distribution of these values is plotted. Each sample is normalized by the median coverage value of that sample to align all peaks with one another and correct for sample-level differences.

Technical Methods

  • Tool Used:

    • Waltz CountReads

    • aggregate_bam_metrics.sh

    • tables_module.py

    • plots_module.r

  • Input

    • Collapsed, unfiltered bam

    • ACCESS pool A bed file

  • Output

    • intervals-coverage-sum.txt (one per bam type / pool combination)

    • coverage_per_interval.txt (one per sample / bam type / pool combination)

    • coverage_per_interval_A_targets_All_Unique.txt (this is used for graph above)

      • (DMP specific format?)

Interpretations Each distribution should be unimodal, apart from a second peak on the low end due to X chromosome mapping from male samples. Narrow peaks are indicative of evenly distributed coverage across all bait regions. Wider distributions indicate uneven read distribution, and may be correlated with a large GC bias. Note that the provided bed file lists start and stop coordinates of ACCESS design probes, not the actual genomic target regions.