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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Contributing Sites for Noise

Understanding how many individual positions lead to noise in the duplex bam

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Last updated 4 years ago

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Theoretical Method

Count the number of positions in the bam that have an alt allele frequency of >0 and <2%

Note: Duplex bams are used for this calculation, and only substitutions are included, not insertions or deletions

Technical Methods

  • Tool Used:

    • Marianas

    • Waltz PileupMetrics

    • calculate_noise.sh (script aggregates across samples from Waltz folder)

  • Input

    • sample_id-duplex-pileup.txt (for duplex noise calculation)

  • Output

    • noise.txt

Interpretations

For the most accurate results, we would like to see lower contributing site values. Higher coverage may lead to more contributing sites for noise.