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Web VEP analysis of variants in Triticum aestivum (wheat)

You have done whole-genome sequencing and variant-calling experiments for Triticum aestivum. You have a VCF file with a small subset of variants from this experiment. Analyse the variants in this file with the VEP tool in Ensembl Plants and determine the following:

  1. How many variants were analysed? How many are novel?

  2. How many genes and transcripts are affected by variants in this file?

  3. Do any of the variants have different consequences for different transcripts?

  4. Filter the table to find variants with high impact. How many variants have high impact? Why do you think missense variants are not classified as high impact?

  5. Can you export all the results to a VCF file? Compare it to the input VCF file to see what information the VEP adds.

Go to any Ensembl Plants page and click on Tools in the navigation bar at the top of the page. Click on Variant Effect Predictor and change your species to Triticum aestivum by clicking on Change species.

Enter a descriptive name for your VEP job. If you have downloaded the variant file to your local machine, click on Choose file to upload. Alternatively, you can paste the URL for the file into the Or provide file URL: box. Click Run at the bottom of the page. When your job is done, click View reesults.

  1. 20 variants were analysed, of which 1 is novel.

  2. Only 1 gene is affected by variants in this file. The gene has 2 transcripts and both are affected by the variants.

  3. You can find a list of calculated variant consequences and their impact here.

    Yes, the novel variant results in a stop_lost in TraesCS3A02G301400.1 and is a downstream_gene_variant for TraesCS3A02G301400.2.

  4. Use the filters to view only variants with HIGH impact (you may need to add the column under Show/hide columns at the top of the table if you cannot find it). The filters are found above the detailed results table in the middle. Select Impact and is from the drop-down menus. Then type HIGH into the box; this will autocomplete. Click Add.

    There are 3 variants with high impact and all three are stop altering. Missense variants are not classified as high impact, because they do not always have significant impacts on protein functions. Usually the protein is still produced. In contrast, stop altering variants affect the protein length, and therefore likely affect the protein function.

  5. At the top right of the table there is an option to download data. Click on VCF for the All option. Open the VCF file you have downloaded in a text editor. You can see that VEP adds annotation in the INFO column of the VCF file.