<div dir="ltr">Hi Konrad,<div><br></div><div>Thanks, this is a bug when using --minimal. This is fixed on release/80 now.</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 7 July 2015 at 14:51, Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org" target="_blank">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">Hi Will/VEP team,<br>
<br>
Found something unexpected when annotating ExAC with VEP v80. The following variant:<br>
<br>
1    139345  .       CGTT    C,TGTT<br>
<br>
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>
<br>
Any information you might have would be very helpful.<br>
<br>
Thanks!<br>
-Konrad<br>
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</blockquote></div><br></div>