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Web VEP analysis of variants in Coffea canephora (coffee)

You have done whole-genome sequencing and variant-calling experiments for Coffea canephora. 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 35246062 var1 C A  
1 35246078 var2 G C
1 35246154 var3 T A

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

  2. Filter the table to find variants with high impact. How many variants have high impact and what consequence predictions do they refer to? Why do you think missense variants are not classified as high impact?

  3. 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. Paste the variants in VCF format into the text box. Click Run at the bottom of the page. When your job is done, click View reesults.

  1. Only 1 gene is affected by variants in this file. The gene has 1 transcript which is affected by the variants.

  2. 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 2 variants with high impact (var1 ands var3). One is a start lost (although also a start retained variant), the other is a splice donor variant. 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, start/stop altering variants affect the protein length, and therefore likely affect the protein function.

  3. 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.