<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></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="">That seems to have fixed a bit (gets through the variant I mentioned before), but still adds ?'s to:</div><div class=""><br class=""></div><div class="">1 224102777 . CTTTTTTTTTTTT CTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTT,C</div><div class=""><br class=""></div><div class="">(Horrifying variant, I know, but does come up!)<br class=""><div class=""><br class="webkit-block-placeholder"></div><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="">Thanks!<br class="Apple-interchange-newline">-Konrad</div></div>
</div>
<br class=""><div><blockquote type="cite" class=""><div class="">On Jul 8, 2015, at 10:38 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 Konrad,<div class=""><br class=""></div><div class="">Thanks, this is a bug when using --minimal. This is fixed on release/80 now.</div><div class=""><br class=""></div><div class="">Will</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On 7 July 2015 at 14:51, Konrad Karczewski <span dir="ltr" class=""><<a href="mailto:konradk@broadinstitute.org" target="_blank" class="">konradk@broadinstitute.org</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Will/VEP team,<br class="">
<br class="">
Found something unexpected when annotating ExAC with VEP v80. The following variant:<br class="">
<br class="">
1 139345 . CGTT C,TGTT<br class="">
<br class="">
seems to annotate without error/warnings, but for some of the entries, ALLELE_NUM is `?` - the first few I checked seem to be upstream_gene_variant and the like, so I'm assuming maybe this means both alleles get the same annotation, but I can't find anything in the documentation.<br class="">
<br class="">
Any information you might have would be very helpful.<br class="">
<br class="">
Thanks!<br class="">
-Konrad<br class="">
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