{"id":12,"date":"2021-04-14T14:01:45","date_gmt":"2021-04-14T14:01:45","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/materials\/template\/day-1\/"},"modified":"2024-06-07T13:03:20","modified_gmt":"2024-06-07T13:03:20","slug":"ensembl-variant-effect-predictor","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/materials\/interpreting-effects-genetic-variants-protein-structure-function\/ensembl-variant-effect-predictor\/","title":{"rendered":"Ensembl \u2013 Variant Effect Predictor"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\"><strong>Trainer: <\/strong>Aleena Mushtaq<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Overview:<\/strong> During the three sections of this course, a single example was used throughout, using different EMBL-EBI tools resources at each stage of the analysis pipeline. In this section, a VCF file was run through <a rel=\"noreferrer noopener\" href=\"https:\/\/www.ensembl.org\/info\/docs\/tools\/vep\/index.html\" target=\"_blank\">the Ensembl Variant Effect Predictor (VEP)<\/a>.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Learning outcomes:<\/strong> <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">After this section you should be able to:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Describe the main functionality and options available for the Ensembl Variant Effect Predictor (VEP)<\/li>\n\n\n\n<li>Annotate a variation dataset using the web-based VEP tool<\/li>\n\n\n\n<li>Interpret the output of the VEP and navigate to other EMBL-EBI resources to further assess variant effects on proteins<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Materials:<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/ftp.ebi.ac.uk\/pub\/training\/2024\/Interpreting_the_effects_of_genetic_variants_on_protein_structure_and_function\/Ensembl_2024-05-24-Interpreting_variants_with_protein_info.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">Interpreting the effects of genetic variants on protein structure and function &#8211; Ensembl slides<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/ftp.ebi.ac.uk\/pub\/training\/2024\/Interpreting_the_effects_of_genetic_variants_on_protein_structure_and_function\/Ensembl_Vep_Demo_May_2024.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">VEP demo<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/ftp.ebi.ac.uk\/pub\/training\/2024\/Interpreting_the_effects_of_genetic_variants_on_protein_structure_and_function\/variants_demo.vcf\" target=\"_blank\" rel=\"noreferrer noopener\">Variants  demo VCF<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/ftp.ebi.ac.uk\/pub\/training\/2024\/Interpreting_the_effects_of_genetic_variants_on_protein_structure_and_function\/variants_practical.vcf\">Practical VCF<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/ftp.ebi.ac.uk\/pub\/training\/2024\/Interpreting_the_effects_of_genetic_variants_on_protein_structure_and_function\/variants_practical_vep_output.vcf\" target=\"_blank\" rel=\"noreferrer noopener\">Practical output VCF<\/a><\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Trainer: Aleena Mushtaq Overview: During the three sections of this course, a single example was used throughout, using different EMBL-EBI tools resources at each stage of the analysis pipeline. In this section, a VCF file was run through the Ensembl Variant Effect Predictor (VEP). Learning outcomes: After this section you should be able to: Materials:<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":1,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-12","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/interpreting-effects-genetic-variants-protein-structure-function\/wp-json\/wp\/v2\/pages\/12","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/interpreting-effects-genetic-variants-protein-structure-function\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/interpreting-effects-genetic-variants-protein-structure-function\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/interpreting-effects-genetic-variants-protein-structure-function\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/interpreting-effects-genetic-variants-protein-structure-function\/wp-json\/wp\/v2\/comments?post=12"}],"version-history":[{"count":13,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/interpreting-effects-genetic-variants-protein-structure-function\/wp-json\/wp\/v2\/pages\/12\/revisions"}],"predecessor-version":[{"id":739,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/interpreting-effects-genetic-variants-protein-structure-function\/wp-json\/wp\/v2\/pages\/12\/revisions\/739"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/interpreting-effects-genetic-variants-protein-structure-function\/wp-json\/wp\/v2\/media?parent=12"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}