Using Import Variants (VCF) (beta) it is possible to import variants in a VCF file to Genotype track format. Below are some significant differences in the way Import Variants (VCF) (beta) handles VCF compared to the standard VCF importer in the workbench:
- If phasing information is encoded in the VCF file as described in the VCF 4.3 specifications (https://samtools.github.io/hts-specs/VCFv4.3.pdf) this information is retained in the Genotype track.
- When filters are specified in the VCF, the corresponding elements in the Genotype track will have applied filters and be hidden as default.
- The option "Optimize for large tracks" allows import of very large VCF files without requiring excessive amounts of memory.
- There is no detection of reference overlap (complex variants) implemented yet.
- It is not possible to import VCF files in batches.
To import variants from VCF to Genotype track format launch the tool Import Variants (VCF) (beta) using the Import button or the Launch button. It is not possible to start the tool from the Toolbox or from Import Tracks from File which is used for standard VCF import.
File | Import () | Import Variants (VCF) (beta)...
In the wizard step Settings specify the VCF file and the Reference Track. For very large VCF files (e.g. dbSNP) check the option Optimize for large tracks. This option allows import of very large files by reducing memory consumption at the cost of speed and disk space.