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VEP analysis of wheat variants

You have done a whole genome sequencing and variant calling experiment 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 and determine:

(a) How many variants were analysed? How many are novel?

(b) How many genes and transcripts are affected by variants in this file?

(c) Do any of the variants have different consequences for different transcripts?

(d) 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?

(e) 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 plants.ensembl.org and click on the link Tools at the top of the page. Click on Variant Effect Predictor and select Species: Triticum aestivum. Either click on Choose file and select the file to upload it, or 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 listed as Done, click View Results.

(a) Twenty variants were analysed, of which one is novel.

(b) Only one gene is affected by variants in this file. It has two transcripts which are both affected.

(c) Yes. The novel variant results in a stop_lost in TraesCS3A02G301400.1 and is a downstream_gene_variant for TraesCS3A02G301400.2.

(d) Use the filters to view only variants with HIGH impact. 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 two variants with high impact and both 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.

(e) 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 the VEP adds annotation in the INFO column of the VCF file.