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<body class='hmmessage'><div dir='ltr'><span style="color: rgb(68, 68, 68); font-size: 15px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">To whom it may concern,</span><div style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-size: 15px; background-color: rgb(255, 255, 255);"><br></div><div style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-size: 15px; background-color: rgb(255, 255, 255);">My name is Manuel Tardaguila and I am an MSC in bioinformatics doing a project in the university of Lausanne. I am working on annotated variations using VEP and snpEff as annotators.</div><div style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-size: 15px; background-color: rgb(255, 255, 255);"><br></div><div style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-size: 15px; background-color: rgb(255, 255, 255);">For frameshift variants I have to calculate downstream effects and I have found this plugin made by your team. I have a question that I would be very grateful if you could address; </div><div style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-size: 15px; background-color: rgb(255, 255, 255);"><span style="line-height: 22.719999313354492px; font-size: 12pt;"><br></span></div><div style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-size: 15px; background-color: rgb(255, 255, 255);"><span style="line-height: 22.719999313354492px; font-size: 12pt;">As happens with other VEP plugins, I suppose that downstream plugin is called from VEP command line when the program is run. In case I have an annotated output from a different program (i.e. snpEff) would it be possible to adapt the plugin or run it separately of VEP?</span></div><div style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-size: 15px; background-color: rgb(255, 255, 255);"><br></div><div style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-size: 15px; background-color: rgb(255, 255, 255);">Thanks in advance for your time and patience,</div><br><div><hr id="stopSpelling">From: manueltar@hotmail.com<br>To: dev@ensembl.org<br>Subject: downstream.pm VEP plugin<br>Date: Mon, 7 Jul 2014 13:33:57 +0200<br><br>
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<div dir="ltr"><span style="color:rgb(68, 68, 68);font-size:15px;line-height:21.299999237060547px;background-color:rgb(255, 255, 255);">Dear Mr Mclaren,</span><div style="line-height:21.299999237060547px;color:rgb(68, 68, 68);font-size:15px;background-color:rgb(255, 255, 255);"><br></div><div style="line-height:21.299999237060547px;color:rgb(68, 68, 68);font-size:15px;background-color:rgb(255, 255, 255);">My name is Manuel Tardaguila and I am an MSC in bioinformatics doing a project in the university of Lausanne. I am working on annotated variations using VEP and snpEff as annotators.</div><div style="line-height:21.299999237060547px;color:rgb(68, 68, 68);font-size:15px;background-color:rgb(255, 255, 255);"><br></div><div style="line-height:21.299999237060547px;color:rgb(68, 68, 68);font-size:15px;background-color:rgb(255, 255, 255);">For frameshift variants I have to calculate downstream effects and I have found this plugin made by your team. I have a question that I would be very grateful if you could address; </div><div style="line-height:21.299999237060547px;color:rgb(68, 68, 68);font-size:15px;background-color:rgb(255, 255, 255);"><span style="line-height:22.719999313354492px;font-size:12pt;"><br></span></div><div style="line-height:21.299999237060547px;color:rgb(68, 68, 68);font-size:15px;background-color:rgb(255, 255, 255);"><span style="line-height:22.719999313354492px;font-size:12pt;">As happens with other VEP plugins, I suppose that downstream plugin is called from VEP command line when the program is run. In case I have an annotated output from a different program (i.e. snpEff) would it be possible to adapt the plugin or run it separately of VEP?</span></div><div style="line-height:21.299999237060547px;color:rgb(68, 68, 68);font-size:15px;background-color:rgb(255, 255, 255);"><br></div><div style="line-height:21.299999237060547px;color:rgb(68, 68, 68);font-size:15px;background-color:rgb(255, 255, 255);">Thanks in advance for your time and patience,</div> </div></div> </div></body>
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