Variant calling accuracy workflow

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:

1. In the Workflow screen, select the Variant analysis/Resequencing tab and choose the “NGS-based” Amplicon, gene panel, exome workflow.

2. 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.

3. In the Input Sequences screen, add read data for the Validation Control.

4. In Assembly Options, check the box next to the desired Variant detection mode.

5. Follow the rest of the wizard screens and initiate the assembly.

6. Variant calling accuracy is evaluated within ArrayStar. Once assembly is complete, see the ArrayStar help topic Validation Control Accuracy for further instructions.