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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Major Contamination

Previous(Un)expected (Mis)matches TablesNextMinor Contamination

Last updated 4 years ago

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Theoretical Method

Major contamination plot is a bar plot of the fraction of heterozygous positions per sample and is done to see if a patient’s sample is contaminated with DNA from an unrelated individual. This analysis also done using the ‘fingerprint’ SNPs in the panel. A SNP is considered heterozygous if the minor allele fraction is > 0.1.

The fraction of heterozygous positions in the sample is found using the formula below:

Fractionheterozygouspositions=(NumberofHeterozygousSites)/(TotalNumberofFingerprintSNPs)Fraction heterozygous positions=(Number of Heterozygous Sites)/(Total Number of Fingerprint SNPs)Fractionheterozygouspositions=(NumberofHeterozygousSites)/(TotalNumberofFingerprintSNPs)

These calculations were done using All Unique (unfiltered) bams. Allele counts are measured from waltz pileups from Pool A and B

Technical Methods

  • Tool Used:

    • Waltz PileupMetrics

    • fingerprinting.py

  • Input

    • output_dir : Directory to write the Output files to

    • waltz_dir_A: Directory with waltz pileup files for target set A

    • waltz_dir_B: Directory with waltz pileup files for target set B

    • waltz_dir_A_duplex: Directory with waltz pileup files for Duplex target set A

    • waltz_dir_B_duplex: Directory with waltz pileup files for Duplex target set B

    • fp_config: File with information about the SNPs for analysis (MSK-ACCESS-v1_0-TilingaAndFpSNPs.txt)

    • title_file: Title File for the run

  • Output

    • FPResults/majorContamination.txt

    • MajorContaminationRate.pdf

Interpretations

The fraction of heterozygous positions should be around 0.5. If the fraction is greater than 0.6, it is is considered to have major contamination.