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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On Target Coverage

Confirming adequate coverage of ACCESS genomic targets

PreviousRaw read-pair counts (standard BAM)NextFraction of reads mapping to the human genome

Last updated 4 years ago

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Theoretical Method

Unlike other coverage metrics from this report which report coverage for bait regions, this graph shows the coverage of actual genomic target regions of the ACCESS A panel

Technical Methods

  • Tool Used:

    • Marianas

    • Waltz CountReads

    • aggregate_bam_metrics.sh

    • tables_module.py

    • plots_module.r

  • Input

    • Duplex Bams

    • pool A bed file

  • Output

    • waltz_duplex_a_exon_level_files (directory of Pool A Exon Targets QC results)

    • waltz-coverage.txt

Interpretations

Coverage in this graph should be slightly higher than for the probe-level coverage results, as the calculation is limited to a smaller window of the histogram of coverage values. This metric is relevant for analysts who are more interested in coverage for a particular gene rather than coverage of the baits used to target that gene.