Using Import VCF to Genotype Track (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 CLC 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 VCF to Genotype Track (beta) using the Launch button or from the Toolbox:
Toolbox | Biomedical Genomics Analysis () | Haplotype Calling (beta) () | Import VCF to Genotype Track (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.