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Hi Eva<br>
<br>
You'll want to put it in as:<br>
8 133984815 133984814 -/TT +<br>
<br>
For insertions, the VEP needs the two bases the insertion falls
between, the highest number first. If you put a space larger than
one base, it doesn't know where the insertion is.<br>
<br>
All the best<br>
<br>
Emily<br>
<br>
<div class="moz-cite-prefix">On 02/03/2015 15:23, Eva Goncalves
Serra wrote:<br>
</div>
<blockquote cite="mid:D11A30F6.15B21%25egs@sanger.ac.uk" type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<div>
<div>
<div>Hi, </div>
<div><br>
</div>
<div>I am trying to use vep75 (with cache) and had to
re-format my input (which was not in vcf/or other compatible
formats) to the ensembl input format. Thought I have done
this successfully but I get an error in a specific
insertion: </div>
<div><br>
</div>
<div>Original file entry:</div>
<div>8:133984814<span class="Apple-tab-span"
style="white-space:pre"> </span>c.6056-29<span
class="Apple-tab-span" style="white-space:pre">
</span>G>GTT</div>
</div>
</div>
<div><br>
</div>
<div>Formatted to ensembl format: </div>
<div>8 133984816 133984814 G/GTT +</div>
<div><br>
</div>
<div>Error I get:</div>
<div>WARNING: start > end+1 : (START=133984816, END=133984814)
on line 19.</div>
<div><br>
</div>
<div>My code to reformat the input was this: </div>
<div><br>
</div>
<div> my @split = split(/\t/); # splitting file by tabs</div>
<div>
<div> my @al = split(':',$split[1]); # getting the chr:pos</div>
<div> my @al2 = split('>',$split[3]); # getting the
ref>alt</div>
<div><br>
</div>
<div> if ((length $al2[0]==1) && (length
$al2[1]==1)) {</div>
<div> print "$al[0] $al[1] $al[1] $al2[0]/$al2[1] +\n";</div>
<div> } elsif (length $al2[1] > length $al2[0]) {</div>
<div> my $sub = (length $al2[1])-(length $al2[0]);</div>
<div> my $new = $al[1]+$sub;</div>
<div> print "$al[0] $new $al[1] $al2[0]/$al2[1] +\n";</div>
<div> } elsif (length $al2[1] < length $al2[0]) {</div>
<div> my $sub2 = (length $al2[0])-(length $al2[1]);</div>
<div> my $new2 = $al[1]-$sub2; </div>
<div> print "$al[0] $new2 $al[1] $al2[0]/$al2[1]
+\n";</div>
<div> }</div>
</div>
<div><br>
</div>
<div>Am I missing something?</div>
<div><br>
</div>
<div>Thanks a lot!</div>
<div><br>
</div>
<div>Eva</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Dr Emily Perry (Pritchard)
Ensembl Outreach Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK </pre>
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