In SeqMan NGen, create a project with the following settings:
1) Welcome screen: Assemble on local computer or Assemble on the DNASTAR cloud.
2) Choose Assembly Workflow: Exome and Gene Panel.
3) Choose Assembly Type: Variant calling accuracy test.
4) Input Reference Sequences: Add the relevant genome package (in most cases, this will be “human”). In the bottom of the screen, leave the VCF file and Targeted regions file boxes checked; they may already be checked, with editing disabled. Then use the associated Browse buttons to locate these files on your computer or in the DNASTAR Cloud Data Drive.
5) Input Sequence Files and Define Experiments or Individual Replicates: Choose the Read technology, then add paired or unpaired read data for the Validation Control.
6) Assembly Options: Check the box next to the desired Variant detection mode.
7) Assembly Output: Enter the Project name and Project folder (required).
8) In the “Your assembly is ready to begin” screen, press Start Assembly. Wait for the assembly to finish.
9) If you performed the assembly on a Windows machine and will be doing the ArrayStar analysis on the same machine, click the Variant Accuracy button to launch ArrayStar and perform the analysis. Otherwise, see the ArrayStar help topic Validation Control Accuracy for further instructions.