While SeqMan NGen 17 no longer has a workflow named “Variant calling accuracy” (AKA “validation control accuracy,” “reference SNP accuracy”), you can still perform this workflow as follows:
- In the Workflow screen, select the Variant analysis/Resequencing tab and choose the “NGS-based” Amplicon, gene panel, exome workflow.
- In the Reference Sequence screen, add the relevant DNASTAR genome package; in most cases, this will be “human”. Check the VCF file and browse to a VCF file of the true variants. If you have a .bed file, you can also check the BED file box (optional) and browse to that file.
- In the Input Sequences screen, add read data for the Validation Control.
- In Assembly Options, check the box next to the desired Variant detection mode.
- Follow the rest of the wizard screens and initiate the assembly.
- Variant calling accuracy is evaluated within ArrayStar. Once assembly is complete, see the ArrayStar help topic Validation Control Accuracy for further instructions.
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