To evaluate the evidence for a called variant, you may select an entry in the ArrayStar SNP table and display the corresponding alignment of sequence reads in SeqMan Pro.
To do this:
1) Close any instance of SeqMan Pro running on your computer.
2) Create or open a Variant comparison project in ArrayStar.
3) Open the SNP Table and locate a row with a variant position of interest. Then select the row and choose File > Send Selection To > SeqMan Pro from the main menu; or right-click on the row and choose Send Selection to SeqMan Pro from the context menu.
4) (multi-experiment project only) If your projects contain multiple experiments, the Choose Experiment dialog opens. Choose the experiment for which you wish to view the variant position and press the OK button.
SeqMan Pro will launch and load the contig containing the selected variant. In the Summary View, the contig will be named as “[project name] [contig name]” (e.g., NA12878_control NC_000001). The Alignment View and SNP Table for that contig will also open to display the point where the variant position is located.
•If you now send another position on the same contig from the same experiment, SeqMan Pro’s Alignment View and SNP Table will move to the new position.
•If you send another position from a different contig from the same experiment, or the same contig from a different experiment, SeqMan Pro will add a new entry to the Summary View and open the corresponding Alignment View and SNP Table.