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QuaC-Watch

QuaC includes a tool called QuaC-Watch, which consumes results from several QC tools, compares QC metrics against the acceptable thresholds, and summarizes results using color-coded pass/fail flags for efficient review. This summary allows users to quickly review output from multiple QC tools, identify whether samples meet expected quality thresholds, and readily highlight samples that need further review.

Configs

We provide pre-defined thresholds for QC metrics as part of the QuaC repo and they need to be supplied via --quac_watch_config:

  • For Genome sequencing - configs/quac_watch/wgs_quac_watch_config.yaml
  • For Exome sequencing - configs/quac_watch/exome_quac_watch_config.yaml

These thresholds were curated based on

  • literature
  • in-house analyses using hundreds of GS and ES samples
  • knowledge gained from our past sample QC experiences

!!! info

QuaC is built to use with Human WGS/WES data. If you would like to use it with non-human data, please modify the pipeline as needed -- especially the thresholds used in QuaC-Watch configs.

Editing configs

If you would like to modify the thresholds, you may use the above-mentioned QuaC-Watch config files as template and then choose the thresholds of your choice. Refer to the tool and QC metric of interest to identify reasonable values to use.

Each QC metric in the config file, except FastQC, requires at least one of minand max values being specified. For example, the snippet below shows thresholds for Qualimap's mean_coverage with minimum value of 30 and maximum value not specified.

qualimap:
  mean_coverage:
    description: "Mean coverage"
    min: 30
    max:

If you would like to specify maximum value, say 50, modify the snippet as follows:

qualimap:
  mean_coverage:
    description: "Mean coverage"
    min: 30
    max: 50

While you may modify the threshold values and description, modifying or removing field names or keys would result in QuaC-Watch behaving in an unexpected manner. For example, the below snippet would fail as it is missing max field.

qualimap:
  mean_coverage:
    description: "Mean coverage"
    min: 30

QuaC-Watch in MultiQC report

QuaC aggregates QC results from multiple tools using MultiQC into a single stand-alone interactive HTML report. QuaC-Watch results are available at the top of this report, and they serve as the first-stop for QC reviewers to quickly check for sample quality. Here is an example screenshot:

QuaC-Watch report

Users may optionally toggle columns to view values for QC metrics of interest and hover over the column title to view thresholds used by Quac-Watch (highlighted by red arrow).