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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UMI Family types Composition (Pool B)

Understanding the relative abundance of each fragment subtype (for Pool B probe regions)

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Last updated 4 years ago

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Theoretical Method

Similarly to the Pool A metrics, the UMI family type composition is here presented for Pool B targets. Buffy coat samples should have comparable UMI family composition for both Pools A and B.

Technical Methods

  • Tool Used:

    • Marianas

    • make_umi_qc_tables.sh

    • plots_module.r

  • Input

    • Marianas collapsed fastqs

  • Output

    • family-types-B.txt

Interpretations

Duplex families are valuable for their low noise rate after collapsing, thus we'd like to see as high of a duplex "saturation" as possible. Because Pool B probes are mixed at a lower ratio in the capture process for cfDNA samples, they will have less duplex saturation. If this value is lower, we may not have captured enough of the original molecules to find both strands after PCR replication.