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Hi Emma,<br>
<br>
When did you pick up the cache files? There was a problem with the
chromosome Y files initially produced for e!77 and they were updated
on the ftp site on 11/11/2014. If you picked them up as soon as they
were released, you may have the broken version.<br>
<br>
We would recommend you switch to a newer version of the code. GRCh37
is still supported and recent versions of VEP are faster than the
version you currently have.<br>
<br>
Best wishes,<br>
<br>
Sarah<br>
<br>
<br>
<div class="moz-cite-prefix">On 01/04/2016 03:02, cy_jiang wrote:<br>
</div>
<blockquote
cite="mid:20160401022427.69D5522D27F_6FDDBDBB@hx-mx1.ebi.ac.uk"
type="cite">
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style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">
<div><span class="" style="color: rgb(0, 0, 0); font-family: 'Helvetica Neue', arial, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 20px; orphans: auto; text-align: left; text-indent: 0px; text-transform: none; white-space: pre-wrap; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none;">Hello there,
I am using the VEP script (version 77) to analyse my variation data locally. It works fine on almost all chromosomes except chrY. For example, variant record "chrY 14107314" got annotation "ENSG00000235649" when using the website VEP, which is correct. However, when I use VEP locally, this record was assigned with "ENSG00000165246". The genome reference I am using is GRCh37.
My command is shown below :</span><span style="color: rgb(0, 0, 0); font-family: 'Helvetica Neue', arial, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 20px; orphans: auto; text-align: left; text-indent: 0px; text-transform: none; white-space: pre-wrap; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none;">
perl /home/software/ensembl-tools-release-77/scripts/variant_effect_predictor/variant_effect_predictor.pl -i input.vcf -o output.vep.vcf –offline –dir_cache /home/data/ensembl/cache –vcf –merged –force_overwrite –quiet –fork 10 –hgvs –assembly GRCh37 –everything
Can anyone give me some clue on this? Thank you very much!
Best,
Emma
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