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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Raw read-pair counts (standard BAM)

Validating the correct number of reads obtained from the sequencer

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Last updated 4 years ago

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Theoretical Method

Total number of reads sequenced. Obtained from iterating through SAMRecord instances in Standard Bam file.

Technical Methods

  • Tool Used

    • Waltz.jar CountReads

    • tables_module.py

    • plots_module.r

  • Input

    • Standard Bam (tables also produced for U / S / D bams)

  • Output

    • Text file with the read count information: “sample_id.bam.read-counts.txt”

Interpretations

ACCESS is designed to target ~50-80M reads per ctDNA sample, and ~5-10M reads for buffy coat samples. This number should be independent of the amount of library input DNA as well as coverage values, as PCR will bring low input values up to a consistent amount for sequencing.