VEP using a VCF file
We have a VCF file with 25 variants in the cow. You can find this file here
(a) Are any of the variants in the file missense variants?
(b) Have any of the missense variants been predicted to be deleterious?
(c) Have the variants been found already?
Go to www.ensembl.org and click on the link Tools at the top of the page. Currently there are six tools for processing your data listed on that page. Click on Variant Effect Predictor and select Species: Cow.
Paste the URL of the file into the box next to Or provide file URL:.You could also paste the content of the file into the box below Either paste data:, or upload the file.
Click Run at the bottom of the page. When your job is listed as Done, click View Results.
You will get a table with the consequence terms from the Sequence Ontology project (i.e. synonymous, missense, downstream) provided by VEP for the listed SNPs, and many other columns.
(a) To see only the missense variants, use a filter: Choose Consequence from the first, and is from from the second drop-down menu. Type missense into the box; this will find missense_variant. Select missense_variant and click Add.
var11, var12, var13, var14, var15, var17 and var23 are missense variants.
(b) SIFT scores are available for missense variants only.
var11 has been predicted to be deleterious, with a SIFT score of 0.01.
(c) To see only known variants, use another filter: Existing variant is defined. Click Add.
All variants have been described previously and have rsIDs.