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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Base Quality Recalibration Scores

Checking for low base quality samples

PreviousUMI Family types Composition (Pool B)NextUMI family sizes (Simplex reads)

Last updated 4 years ago

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Theoretical Method

The sequencer uses the difference in intensity of the fluorescence of the bases to give an estimate of the quality of the base that has been read. The BaseQualityScoreRecalibration (BQSR) tool from GATK recalculates these values based on the empirical error rate of the reads themselves, which is a more accurate estimate of the original quality of the read.

Technical Methods

  • Tool Used:

    • GATK BaseQualityScoreRecalibration

    • Picard MeanQualityByCycle

  • Input

    • Standard, Uncollapsed Bams

  • Output

    • sample_id.bam.quality_by_cycle_metrics

    • sample_id.bam.quality_by_cycle.pdf

Interpretations

It is normal to see a downwards trend in pre and post-recalibration base quality towards the ends of the reads. Average post-recalibration quality scores should be above 20. Spikes in quality may be indicative of a sequencer artifact.