In Part A, you created a validation assembly in SeqMan NGen. In this part, you will learn how to import the SeqMan NGen assembly into ArrayStar and then run the validation control analysis.

When SeqMan NGen and ArrayStar are on the same Windows machine:

If you are running a local SeqMan NGen assembly on Windows and have ArrayStar on the same machine, you can perform the analysis automatically.

  1. Wait until the assembly process has finished, then click Next.

  1. In the SeqMan NGen Project Report screen, click the Variant Accuracy button.

ArrayStar will launch the validation control sample, load the associated VCF file automatically, and run the validation statistics. Continue to “The Validation Control Accuracy Report,” this topic.

All other situations:

If you are running the assembly on Macintosh or the Cloud, you must set up the ArrayStar project manually.

  1. Wait until the assembly process has finished, then click Next.
  1. Launch ArrayStar manually.
  1. From the Welcome screen, click on Start a new project. Choose Variant comparison and click Next.
  1. In the Add Experiments to Import screen, click Add SeqMan NGen .assembly folder and load the NA12878.assembly.
  1. Click Next and continue through the setup screens, leaving everything at the default values. On the last screen, press Finish.
  1. Once the setup wizard closes, choose Statistics > Validation Control Accuracy.
  1. In the Statistics Parameters dialog, leave the default settings (Standard = NA12878 VCF NA12878 and Validation Control = NA12878).
  1. Press Calculate to begin the Validation Control Accuracy calculation.

Once the calculation is complete, the Validation Control Accuracy report is displayed.

The Validation Control Accuracy Report:

Each calculation in the report is accompanied by a helpful text description. For detailed information on interpreting the report, see the ArrayStar online help topic The Validation Control Accuracy Report.

Use File > Save Project to save the ArrayStar project as T5_Validation_Control.astar.

Congratulations on completing Tutorial 5. For a complete list of our other available tutorials, click here.

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