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<div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">
Hi Wei,</div>
<div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">
<br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Sorry for the delay, I had an email typed out, but got stuck because I couldn't figure out what was going on with the first variant (which is missing from ExAC). I see now that it's probably a typo and you probably meant 245133629.</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><div id="bloop_customfont" style="margin: 0px;"><br></div><div id="bloop_customfont" style="margin: 0px;">In any case, indeed I'm getting different results. Can you post your annotated output of the variants here?
Specifically, why they get an LC mark. If it's NON_CAN_SPLICE, I suspect there may be an issue with the FASTA index that is sending LOFTEE a sequence of "NN" for the splice site and making it think it's a non-GT/AG splice site.</div></div>
<div><br></div>Thanks,<br>
<div id="bloop_sign_1457907324881916160" class="bloop_sign">
<div style="font-family:helvetica,arial;font-size:13px">
-Konrad</div>
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<br>
<p class="airmail_on">On March 13, 2016 at 6:14:52 PM, Wei Zhao
(<a href="mailto:mikezhaow@gmail.com">mikezhaow@gmail.com</a>)
wrote:</p>
<blockquote type="cite" class="clean_bq">
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<div><span>Dear Konrad,<br>
<br></span></div>
<div><span>I have some variant-transcript pairs and the LOFTEE
annotations I got by running it locally and checking ExAc website
are different: ExAc reported "high-confidence" while I got
"LC". It seems to me that all of these variants are related
to splicing and I listed three examples below. Could you
please kindly take a look? Hope I didn't miss anything
obvious. I was running VEPv83 and downloaded LOFTEE on March
9th.<br></span></div>
<div><span><br></span></div>
<div><span>Thank you for you help.<br>
<br></span></div>
<div><span>Best,<br></span></div>
<div><span>Wei<br></span></div>
<div><span><br>
1:2451336129_A/G, ENST00000366523<br></span></div>
<span>5:177474136_T/C, ENST00000511189<br></span></div>
<span>8:130789839_T/C, <a href="http://exac.broadinstitute.org/transcript/ENST00000276708">ENST00000276708</a><br>
<br>
<br></span></div>
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</blockquote>
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