VEP analysis of variant in Atlantic salmon
You have performed sequencing and variant-calling experiments for Atlantic salmon. You have a few variants in the VCF format from this experiment:
25 4297825 . G A.
25 4293985 . C G.
25 4294047 . G T.
25 4294047 . G T.
25 4270019 . G A.
(a) How many variants were analysed? How many are novel?
(b) How many genes and transcripts are affected by these variants?
(c) Do any of the variants have different consequences for different transcripts?
(d) Can you export all the results to a VCF file?
Go to www.ensembl.org and click on the Variant Effect Predictor link on the homepage. Click Launch VEP.
Choose Atlantic salmon as the species and enter the five variants from the exercise.
Note: Variation data input can be done in a variety of formats. See more details here http://www.ensembl.org/info/docs/variation/vep/vep_formats.html
Click Run.
When your job is listed as Done, click View Results.
(a) Five variants were analysed, none of these variants are novel.
(b) Only one gene (cdc16) is affected by these variants. It has ten transcripts, all of which are affected.
(c) Yes. These variants have the missense_variant, intron_variant and downstream_gene_variant consequences for the different transcripts of cdc16 gene.
(d) 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.
