Access Quality Control (v2)
MSK-ACCESS QC generation V2
add-qc-workflowdevelopMSK-ACCESS QC generation V2
MSK-ACCESS QC generation V2
add-qc-workflowdevelopMSK-ACCESS QC generation V2
  • MSK-ACCESS QC generation
  • Installation and Running
    • Requirements
    • Installation and Usage
    • Inputs Description
  • Interpretation
    • Sample meta information
    • Coverage vs GC bias
    • Insert size metrics
    • Target coverage distribution
    • Capture metrics
    • Duplex family metrics
    • Mean base quality
    • Duplex noise metrics
    • Contamination
    • Fingerprinting
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  • Introduction
  • Methods
  • Interpretation

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  1. Interpretation

Capture metrics

Validating the efficacy of the Pool A and Pool B bait sets.

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Last updated 3 years ago

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Introduction

There are several sections displaying bait set capture efficiency. Each section corresponds to a separate BAM type and bait set combination. The tool used to produce the metrics is GATK-CollectHsMetrics. By default, only the mean bait coverage, mean target coverage, and % Usable bases on-target are displayed. However, there are many more metrics that can be toggled to display by clicking on the Configure Columns button.

Methods

Interpretation

The aim is to have high coverage across Pool A and Pool B panels.

Tool used: BAM type: (1) Uncollapsed BAM, (1) Collapsed BAM, (1) Duplex BAM, and (4) Simplex BAM Regions: Pool A and Pool B

GATK-CollectHsMetrics
Example MultiQC report showing insert size distribution for 20 samples (10 plasma and 10 buffy coat samples).