By default, SeqMan NGen chooses the longest CDS as the isoform for SNP calling. If desired, you may override the automated choice by specifying the preferred isoform manually in the template sequence.
To do so, follow these steps prior to importing the template sequence into SeqMan Wizard’s Input Reference Sequences screen:
1) Open the template (reference) sequence in a text editor.
2) Locate the feature of interest. Just below its location coordinates, type in /dnas_isoform.
3) Save the edited template sequence.
4) Input the saved version of the template sequence into SeqMan Wizard’s Input Reference Sequences screen.