<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Will,<div class=""><br class=""></div><div class="">Along these lines, however, VEP doesn't seem to be writing ALLELE_NUM properly on these lines (particularly when the * is not last in the list).</div><div class=""><br class=""></div><div class="">For instance, when annotating this (VEP v81 and 82):</div><div class=""><br class=""></div><div class="">1 874817 rs201898716 C *,T</div><div class=""><br class=""></div><div class="">it gives the same output as if the ALT were T,*</div><div class=""><br class=""></div><div class="">Hope it's an easy fix!<div apple-content-edited="true" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">-Konrad</div></div>
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<br class=""><div><blockquote type="cite" class=""><div class="">On Nov 16, 2015, at 12:36 PM, JESSICA X. CHONG <<a href="mailto:jxchong@uw.edu" class="">jxchong@uw.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Ahhh ok, this makes sense to find the annotation on the previous line.
<div class=""><br class="">
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<div class="">Thanks.</div>
<div class=""><br class="">
<div class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On Nov 16, 2015, at 3:00 AM, Will McLaren <<a href="mailto:wm2@ebi.ac.uk" class="">wm2@ebi.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hi Jessica,
<div class=""><br class="">
</div>
<div class="">The * allele is not annotated because there is nothing to annotate; it represents the absence of any allele due to an upstream deletion. The upstream deletion will of course be annotated.</div>
<div class=""><br class="">
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<div class="">Example:</div>
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</div>
<div class=""><font face="monospace, monospace" class="">REF: ACGGTAGC</font></div>
<div class=""><font face="monospace, monospace" class="">S1 : ACG----C</font></div>
<div class=""><font face="monospace, monospace" class="">S2 : ACGGCAGC</font></div>
<div class=""><font face="monospace, monospace" class=""><br class="">
</font></div>
<div class=""><font face="arial, helvetica, sans-serif" class="">There are two mutations here; one deletion in S1, and one SNP in S2. Because the sequence containing the SNP is absent in S1, the genotype calls for this site in individuals with the deletion
are otherwise impossible to annotate, unless you use the * notation.</font></div>
<div class=""><font face="arial, helvetica, sans-serif" class=""><br class="">
</font></div>
<div class=""><font face="arial, helvetica, sans-serif" class="">So the VCF looks like this:</font></div>
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</div>
<div class=""><font face="monospace, monospace" class="">chr1 3 GGTAG G ... 1/1 0/0</font></div>
<div class=""><font face="monospace, monospace" class="">chr1 5 T C,* ... 2,2 1/1</font></div>
<div class=""><font face="monospace, monospace" class=""><br class="">
</font></div>
<div class=""><font face="arial, helvetica, sans-serif" class="">VEP will annotate the deletion as normal, but will only annotate the C ALT allele for the SNP; the * represents the absence of an allele, so no annotation is added - the deleted sequence is annotated
for the variant on the previous line.</font></div>
<div class=""><font face="arial, helvetica, sans-serif" class=""><br class="">
</font></div>
<div class=""><font face="arial, helvetica, sans-serif" class="">Hopefully that makes sense!</font></div>
<div class=""><font face="arial, helvetica, sans-serif" class=""><br class="">
</font></div>
<div class=""><font face="arial, helvetica, sans-serif" class="">If you can provide an example of where you think VEP is doing something wrong then of course please do let us know.</font></div>
<div class=""><font face="arial, helvetica, sans-serif" class=""><br class="">
</font></div>
<div class=""><font face="arial, helvetica, sans-serif" class="">Regards</font></div>
<div class=""><font face="arial, helvetica, sans-serif" class=""><br class="">
</font></div>
<div class=""><font face="arial, helvetica, sans-serif" class="">Will McLaren</font></div>
<div class=""><font face="arial, helvetica, sans-serif" class="">Ensembl Variation</font></div>
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<div class="gmail_extra"><br class="">
<div class="gmail_quote">On 13 November 2015 at 21:35, JESSICA X. CHONG <span dir="ltr" class="">
<<a href="mailto:jxchong@uw.edu" target="_blank" class="">jxchong@uw.edu</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<a href="http://gatkforums.broadinstitute.org/discussion/6240/what-means-is-in-alternative-allele" rel="noreferrer" target="_blank" class="">http://gatkforums.broadinstitute.org/discussion/6240/what-means-is-in-alternative-allele</a><br class="">
<br class="">
Apparently GATK now uses * to represent long “upstream deletions.”<br class="">
<br class="">
It looks like as of v82, VEP cannot handle annotation of * alleles. The lines in the resulting VCF completely lack VEP’s CSQ field.<br class="">
<br class="">
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