{"id":109,"date":"2014-11-22T23:21:44","date_gmt":"2014-11-22T22:21:44","guid":{"rendered":"http:\/\/ist.blogs.inra.fr\/wdi\/?page_id=109"},"modified":"2015-09-17T15:56:20","modified_gmt":"2015-09-17T14:56:20","slug":"use-of-the-snpeff-software","status":"publish","type":"page","link":"https:\/\/ist.blogs.inrae.fr\/wdi\/use-of-the-snpeff-software\/","title":{"rendered":"Decipher the effect of SNPs"},"content":{"rendered":"<h2 style=\"color: #33aabd\">Description<\/h2>\n<p>Several softwares can be used:<\/p>\n<ul>\n<li>Variant Effect Predictor (<a href=\"http:\/\/www.ensembl.org\/info\/docs\/tools\/vep\/index.html\">VEP from EBI<\/a>)<\/li>\n<li><a href=\"http:\/\/snpeff.sourceforge.net\/\">SnpEff<\/a>\u00a0is a genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).<\/li>\n<\/ul>\n<p>In this example, we use SnpEff.<\/p>\n<h2 style=\"color: #33aabd\">Data\u00a0types<\/h2>\n<h4><b>Inputs<\/b><\/h4>\n<p>SNP discovery VCF file and Genome annotation GFF3 file.<\/p>\n<h4><b>Output<\/b><\/h4>\n<p>Enriched VCF file with the SNP effect on genes.<\/p>\n<h2 style=\"color: #33aabd\">Challenges<\/h2>\n<p>Choose the same reference sequence and select the proper amino acid code.<\/p>\n<h4><b>Recommendation<\/b><\/h4>\n<p>Use the wheat survey sequence as the reference sequence for the moment. When the complete wheat genome is sequenced (in 3 years at the earliest), it make it possible to remap the SNPs on the new reference.<\/p>\n<p>Select VCF as output format.<\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #33aabd\">Writing:<\/span>\u00a0Michael Alaux, Nacer Mohellibi, Loic Couderc<\/p>\n<p><span style=\"color: #33aabd\">Creation date:<\/span>\u00a002 October 2014<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Description Several softwares can be used: Variant Effect Predictor (VEP from EBI) SnpEff\u00a0is a genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes). In this example, we use SnpEff. Data\u00a0types Inputs SNP discovery VCF file and Genome annotation GFF3 file. Output Enriched [&hellip;]<\/p>\n","protected":false},"author":11,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"open","ping_status":"open","template":"","meta":{"footnotes":""},"class_list":["post-109","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/pages\/109","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/users\/11"}],"replies":[{"embeddable":true,"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/comments?post=109"}],"version-history":[{"count":0,"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/pages\/109\/revisions"}],"wp:attachment":[{"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/media?parent=109"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}