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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Insert Size Distribution

Confirmation of fragment length information for cfDNA and buffy coat DNA fragments

PreviousCoverage vs GC contentNextDistribution of ACCESS panel A coverage values

Last updated 4 years ago

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Theoretical Method

Insert size is calculated from the start and stop positions of the reads after mapping to the reference genome.

Technical Methods

  • Tool Used:

    • Waltz CountReads

    • aggregate_bam_metics.sh

    • tables_module.py

    • plots_module.r

  • Input

    • Collapsed all unique bam

    • ACCESS pool A bed file

  • Output

    • sample_id.bam.fragment-sizes

    • fragment_sizes.txt (aggregated across samples from a single bam type / pool combination)

    • fragment_sizes_unfiltered_A_targets.txt (used for graph above)

Interpretations Cell free DNA has distinctive features due to the natural processes behind its fragmentation. One such feature is the set of 10-11 bp fluctuations that indicate the preferential splicing of fragments due to the number of bases per turn of the DNA helix, which causes a unique pattern of binding to the surface of histones.

The more pronounced peak at 166 bp indicate complete wrapping of the DNA around the histones’ circumference, and similarly the second more pronounced peak indicates two complete wraps.

Buffy coat samples are mechanically sheared and thus do not exhibit these distinctive features, hence the different shape for their distribution.

Note: All values are shifted 6 bp lower, due to clipping of 3 bp from each end of the reads during the collapsing process