Ensembl Plants VEP
Use the established web or command-line VEP when your species and assembly are supported. Tomato students should confirm that variants and annotation both use SL4.0 before submission.
VCF checker and summary
Paste text or choose an uncompressed VCF. The file stays in your browser.
Maximum 2 MB.
| Measure | Value |
|---|
Records per chromosome
None
Malformed lines
Run the checker to see line-level errors.
CDS consequence explorer Experimental
Teaching aid, not a replacement for VEP. It supports simple DNA SNVs/indels in phase-0 CDS rows, the standard nuclear genetic code, and a two-base splice-site flag. It is not HGVS, does not normalize variants, and omits UTR, regulatory, structural, haplotype, alternative-code and complex transcript logic.
Each input is limited to 2 MB and processed locally.
| Chromosome | Position | Allele | Transcript | Consequence | Near splice boundary |
|---|
Where to annotate at scale
fastVEP
For custom organisms or local workflows, fastVEP accepts VCF with a matching GFF3 and FASTA. The hosted service is intended for interactive use; its documentation directs bulk jobs to the self-hosted CLI.
File-preparation checklist
- Record the exact assembly and gene-model release; “tomato” alone is not enough.
- Use the same FASTA used for read alignment and variant calling.
- Make contig names agree across VCF, FASTA and GFF3 (for example,
1versuschr1). - Left-normalize and split multiallelic records with a standard workflow before comparing annotators.
- Keep REF alleles consistent with the FASTA; retain sample/genotype columns if they matter downstream.
- Start with a few variants whose locations you can inspect, then run the full file locally.
Practical use
After resequencing, GWAS or CRISPR editing, consequence annotation helps prioritize variants overlapping gene models. It does not establish causality: inspect transcript choice, allele frequency, segregation, expression, off-target evidence and biological validation separately.
How to use
- Start in VCF checker and resolve malformed lines.
- Use the Experimental explorer only for a small, known teaching model, or skip directly to the scale guide.
- Confirm research results with Ensembl Plants VEP, fastVEP CLI, or another maintained full annotator.
Limitations
The checker validates a useful subset of VCF structure, not the complete VCF specification. Ts/Tv counts simple A/C/G/T SNP alleles; a zero-transversion ratio is shown as undefined. The experimental predictor does not claim parity or measured accuracy against Ensembl VEP or fastVEP. Inputs and results are not sent anywhere.
Frequently asked questions
Does this upload my files?
No. Processing stays in your browser, and this page's policy blocks network connections.
Can I use a whole-genome VCF?
No. The 2 MB cap is for quick teaching and preflight checks. Use a command-line annotator for large files.
Is this HGVS or clinically validated?
No. It does not generate HGVS and is not for clinical interpretation.
Why do assembly names matter?
Coordinates, REF alleles and gene models only align when all inputs describe the same assembly and contig naming scheme.
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