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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Fraction of reads mapping to the human genome

Ensure there is adequate mapping of sequenced reads to the human genome

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Last updated 4 years ago

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Theoretical Method

This metric is obtained by iterating through the bam file, and looking at the sam flag which indicates whether each read has an adequate mapping to the HG19 reference.

Technical Methods

Waltz uses a method from the SAMRecord Class of the HTSJDK library:

SAMRecord.getReadUnmappedFlag()

Note: This method is distinct from getProperPairFlag(),which will only consider reads which are mapped in a proper pair.

  • Tool Used

    • waltz.jar CountReads

    • Aggregate_bam_metrics.sh

    • tables_module.py (TotalMapped / TotalReads)

    • plots_module.r

  • Input

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

  • Output

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

Interpretations

Mapping fraction to the human genome should be above 97%, in most cases if it is below that, there is a chance that there is contamination from another species.

Note: this metric come from the standard bam, and is calculated across the entire bam file (as opposed to pool A or pool B on their own)