<div dir="ltr">Hi Will,<div><br><div>Thanks - reinstalling the cache worked. </div></div><div><br></div><div>Best</div><div>Jenn</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jun 25, 2015 at 7:54 AM, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Jenn,<div><br>Can you provide more details of this please?</div><div><br></div><div>- Which VEP version are you using?</div><div>- which cache (GRCh37 or GRCh38, RefSeq or Ensembl or merged)?</div><div>- have you run <a href="http://convert_cache.pl" target="_blank">convert_cache.pl</a>?</div><div><br></div><div>If possible are you able to provide a sample of input and a command line that reproduces this error?</div><div><br></div><div>If the error occurs with the example_GRCh3*.vcf files provided alongside the script, I'd try re-installing VEP and the cache.</div><div><br></div><div>Thanks</div><div><br>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On 24 June 2015 at 17:54, Jennifer Yen <span dir="ltr"><<a href="mailto:jennifer.yen@personalis.com" target="_blank">jennifer.yen@personalis.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr">Hi Will,<div><br><div>The --check_alleles flag generates an error when it starts checking for existing variations. ("Use of uninitialized value in list assignment at VEP.pm line 5130, <DUMP>".) The vep script runs fine without the flag though - anyone else have problems with this?</div><div><br></div><div>Jenn</div>
</div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jun 24, 2015 at 12:54 AM, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello Mollie,<div><br></div><div>The VEP can compare the alleles of your input with those from the rs# variants; select "Yes and compare alleles" from the "Find co-located known variants:" dropdown menu under the "Identifiers and frequency data" tab when you submit your job.</div><div><br></div><div>In the standalone tool, you must add the "--check_alleles" flag.</div><div><br></div><div>Online: <a href="http://www.ensembl.org/info/docs/tools/vep/online/input.html#ident" target="_blank">http://www.ensembl.org/info/docs/tools/vep/online/input.html#ident</a></div><div>Standalone: <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_check_existing" target="_blank">http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_check_existing</a></div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 23 June 2015 at 20:22, Ullman-Cullere, Mollie <span dir="ltr"><<a href="mailto:MULLMANCULLERE@partners.org" target="_blank">MULLMANCULLERE@partners.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">The rs# is a location identifier, where theoretically one rs# may have multiple variants A/T, A/C, A/G. To muddy the waters further, you may have A/T somatic, A/T germline etc...<br>
<br>
I've been testing VEP GRCh 37 (online version) and found the rs# is returned on a matching of location and not location + nucleotide change.<br>
Would you please confirm functionality for both the online and standalone tools?<br>
<br>
Best regards,<br>
Mollie<br>
<br>
Mollie Ullman-Cullere<br>
Sr. Clinical Bioinformaticist<br>
Clinical and Translational Informatics<br>
Dana-Farber Cancer Institute/Partners Healthcare<br>
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