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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Introduction

NextMeta information per sample

Last updated 4 years ago

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MSK-ACCESS Quality Control (QC) Version 1 (v1) is intended to ensure all samples are processed in an accurate and consistent manner using the workflow.

The following pages give descriptions on how to interpret Quality Control metrics presented in the PDF report, page by page.

Here is an example Quality Control report for the V1 :

Note: All output sections in the following pages will refer to files found in the QC_Results folder from a V1 ACCESS pipeline run.

The subfolders are named as: waltz_<bam_type>_<pool_A_or_B>_(exon_level_files)?

There will be 12 such subfolders, and each will contain a copy of that metrics file, for the specific combination of bam type and Pool (which may be either target-specific or bait-specific) that is listed.

https://github.com/mskcc/ACCESS-Pipeline
ACCESS pipeline
357KB
09780_B_2020-06-10_22-42-38.pdf
pdf
09780_B