In the Input Reference Sequences screen, certain workflows offer some subset of the following options.

  • Include alternative assembly templates – (only available if a genome package was selected) Check the box to include an alternate sequence representation for variant regions, also referred to as “alternate locus” or “alt loci.” Alternate sequences include those known to be in a particular chromosome, but whose exact position is unknown; and sequences with known positions, but otherwise incomplete entries. For definitions and additional information, see these Genome Reference Consortium web pages: Announcement (“Variation” section) and Definitions (particularly, “alternate locus”, “unlocalized sequence” and “unplaced sequence”).
  • VCF file - Certain SeqMan NGen workflows allow or require you to import a custom VCF SNP file|topic=Make a Custom VCF File with data from one or more assemblies. To add a VCF file, check the box next to VCF file and then use the corresponding Browse button to navigate to the file. If you elect to do this, positions within the VCF file will be given a VCF SNP ID during the assembly process. After assembly, information about each position can be viewed in the SeqMan Pro SNP Report. (Within SeqMan Pro, choose SNP > SNP Report.)

    • For local assemblies, Browse launches your file explorer. Navigate to the VCF file and then click Open.

    • For Cloud assemblies, Browse launches the Cloud Data Drive. Navigate to the VCF file and then click the green check mark ().
  • Targeted Regions file - If you chose Exome and Gene Panel from the Choose Assembly Workflow screen, this checkbox will be checked by default. You cannot proceed to the next screen until you have specified a file containing targeted region information. BED files must have the extension .bed. Manifest files can have various extensions, but must be in the correct format.

    • For local assemblies, Browse launches your file explorer. Navigate to the BED or manifest file and then click Open.

      For Cloud assemblies, Browse launches the Cloud Data Drive. Navigate to the BED or manifest file and then click the green check * mark ().

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