Certain workflows allow or require you to import a BED file, Manifest file, or a custom VCF SNP file with data from one or more assemblies. These options, if available, will be offered at the bottom of the Reference Sequence screen.
To add a BED, Manifest, or targeted regions file:
These files can be used in many types of assemblies, and should always be uploaded when doing exome assemblies.
To add a file of these types, check the box next to BED file and then use the corresponding Browse button to navigate to the file. If you are doing a local assembly, select the file and click Open. If you are doing a Cloud assembly, select the file and click the green check mark (
). Note that:
- You must upload the .bed file from the capture kit, not any random .bed file. For instance, if you used Human Genome build 38 as the reference, for example, the corresponding .bed file might be called Human genome build38.bed. Sequencing services do not always send the .bed file to customers, but can often provide it on request.
- BED files must have the extension .bed. For information on making a BED file, see Make a custom BED file.
- Manifest files are typically used to represent coordinates of regions that were captured in procedures, such as exon capture performed prior to sequencing. They can have various extensions (usually .txt), but must be in the correct format.
To add a VCF file:
Most users will not have a VCF file to upload, but are looking forward to producing a VCF file as part of the assembly output. However, researchers working with standard reference data sets may have a VCF file to upload to the wizard at this stage.
To upload a VCF file, check the box next to VCF file and then use the corresponding Browse button to navigate to the file. If you are doing a local assembly, select the file and click Open. If you are doing a Cloud assembly, select the file and click the green check mark (). 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 (SNP > SNP Report) or the SeqMan Ultra Variants view. SeqMan NGen only supports one VCF file per assembly project. If you have multiple VCF files (e.g., one per chromosome), you must merge the information into a single VCF file before browsing to the file. For more information, see Make a custom VCF file.
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