<span id="mailbox-conversation"><div>Hi Will,</div>
<div><br></div>
<div>Thanks! If it's not too much trouble to push to 81, that'd be great (I haven't tested 82 too much yet). If it's annoying though, don't worry about it.</div>
<div><br></div>
<div>Thanks!</div></span><div class="mailbox_signature">
<br>-Konrad</div>
<br><br><div class="gmail_quote"><p>On Wed, Nov 18, 2015 at 8:18 AM, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br></p><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div>
<div dir="ltr">Hi Konrad,<div><br></div>
<div>Thanks, this is fixed on 82.</div>
<div><br></div>
<div>I can push to 81 too if you need?</div>
<div><br></div>
<div>Will</div>
</div>
<div class="gmail_extra">
<br><div class="gmail_quote">On 17 November 2015 at 01:42, Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org">konradk@broadinstitute.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Will,<div><br></div>
<div>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><br></div>
<div>For instance, when annotating this (VEP v81 and 82):</div>
<div><br></div>
<div>1 874817 rs201898716 C *,T</div>
<div><br></div>
<div>it gives the same output as if the ALT were T,*</div>
<div><br></div>
<div>Hope it's an easy fix!<span class="HOEnZb"><font color="#888888"><div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><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;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">-Konrad</div></div>
</div></font></span><div><div class="h5">
<br><div><blockquote type="cite">
<div>On Nov 16, 2015, at 12:36 PM, JESSICA X. CHONG <<a href="mailto:jxchong@uw.edu">jxchong@uw.edu</a>> wrote:</div>
<br><div>
<div style="word-wrap:break-word">
Ahhh ok, this makes sense to find the annotation on the previous line.
<div><br></div>
<div>Thanks.</div>
<div>
<br><div>
<div>
<blockquote type="cite">
<div>On Nov 16, 2015, at 3:00 AM, Will McLaren <<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>> wrote:</div>
<br><div>
<div dir="ltr">Hi Jessica,
<div><br></div>
<div>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><br></div>
<div>Example:</div>
<div><br></div>
<div><font face="monospace, monospace">REF: ACGGTAGC</font></div>
<div><font face="monospace, monospace">S1 : ACG----C</font></div>
<div><font face="monospace, monospace">S2 : ACGGCAGC</font></div>
<div><font face="monospace, monospace"><br></font></div>
<div><font face="arial, helvetica, sans-serif">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><font face="arial, helvetica, sans-serif"><br></font></div>
<div><font face="arial, helvetica, sans-serif">So the VCF looks like this:</font></div>
<div><br></div>
<div><font face="monospace, monospace">chr1 3 GGTAG G ... 1/1 0/0</font></div>
<div><font face="monospace, monospace">chr1 5 T C,* ... 2,2 1/1</font></div>
<div><font face="monospace, monospace"><br></font></div>
<div><font face="arial, helvetica, sans-serif">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><font face="arial, helvetica, sans-serif"><br></font></div>
<div><font face="arial, helvetica, sans-serif">Hopefully that makes sense!</font></div>
<div><font face="arial, helvetica, sans-serif"><br></font></div>
<div><font face="arial, helvetica, sans-serif">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><font face="arial, helvetica, sans-serif"><br></font></div>
<div><font face="arial, helvetica, sans-serif">Regards</font></div>
<div><font face="arial, helvetica, sans-serif"><br></font></div>
<div><font face="arial, helvetica, sans-serif">Will McLaren</font></div>
<div><font face="arial, helvetica, sans-serif">Ensembl Variation</font></div>
</div>
<div class="gmail_extra">
<br><div class="gmail_quote">On 13 November 2015 at 21:35, JESSICA X. CHONG <span dir="ltr">
<<a href="mailto:jxchong@uw.edu">jxchong@uw.edu</a>></span> wrote:<br><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">http://gatkforums.broadinstitute.org/discussion/6240/what-means-is-in-alternative-allele</a><br><br>
Apparently GATK now uses * to represent long “upstream deletions.”<br><br>
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><br><br>
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