<div dir="ltr">Hi Martin,<div><br></div><div>Thanks for finding this - there was a bug in the sorting method.</div><div><br></div><div>I've pushed a fix to GitHub on the release/75 branch, are you able to update your API checkout, or rerun INSTALL.pl to pick up the fixed API?</div>
<div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 28 March 2014 13:55, Martin Pollard <span dir="ltr"><<a href="mailto:mp15@sanger.ac.uk" target="_blank">mp15@sanger.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 style="word-wrap:break-word"><div style="margin:0px;font-size:11px;font-family:Menlo">Hi,</div><div style="margin:0px;font-size:11px;font-family:Menlo">
<br></div><div style="margin:0px;font-size:11px;font-family:Menlo">I’m having a problem with a specific VCF file. I have run it through the VEP perl script twice and for some reason it reorders the VCF file so that part of chromosome 9 ends up interleaved with chromosome 10 in the VCF file. The strange thing being that it’s happened in exactly the same region in the file.</div>
<div style="margin:0px;font-size:11px;font-family:Menlo"><div style="margin:0px"><br></div><div style="margin:0px">9 BEGIN-139307194</div></div><div style="margin:0px;font-size:11px;font-family:Menlo"><div style="margin:0px">
10<span style="white-space:pre-wrap"> </span>93528-38598955</div><div style="margin:0px">9<span style="white-space:pre-wrap"> </span>139308932-141071552</div><div style="margin:0px"><div style="margin:0px">10<span style="white-space:pre-wrap"> </span>38599101-END</div>
</div></div><div style="margin:0px;font-size:11px;font-family:Menlo"><br></div><div style="margin:0px;font-size:11px;font-family:Menlo">Any suggestions?</div><div style="margin:0px;font-size:11px;font-family:Menlo"><br></div>
<div style="margin:0px;font-size:11px;font-family:Menlo">Martin</div><div style="margin:0px;font-size:11px;font-family:Menlo"><br></div><div style="margin:0px;font-size:11px;font-family:Menlo">Command used:</div><div style="margin:0px;font-size:11px;font-family:Menlo">
<div style="margin:0px">perl /nfs/users/nfs_m/mercury/src/ensembl-tools-release-75/scripts/variant_effect_predictor/<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -i all.vqsr.dbsnp.vcf.gz -o all.vqsr.dbsnp.vep2.vcf --vcf -cache -dir_cache /data/blastdb/Ensembl/vep</div>
</div><div style="margin:0px;font-size:11px;font-family:Menlo"><br></div><div style="margin:0px;font-size:11px;font-family:Menlo">Version info:</div><div style="margin:0px;font-size:11px;font-family:Menlo"><br></div><div style="margin:0px;font-size:11px;font-family:Menlo">
<div style="margin:0px"># ENSEMBL VARIANT EFFECT PREDICTOR #</div><div style="margin:0px">version 75</div><div><div style="margin:0px"><br></div><div style="margin:0px">Linux bc-19-3-01 2.6.32-44-server #98-Ubuntu SMP Mon Sep 24 17:41:33 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux</div>
</div><div><div style="margin:0px"><br></div><div style="margin:0px">Distributor ID:<span style="white-space:pre-wrap"> </span>Ubuntu</div><div style="margin:0px">Description:<span style="white-space:pre-wrap"> </span>Ubuntu 12.04.2 LTS</div>
<div style="margin:0px">Release:<span style="white-space:pre-wrap"> </span>12.04</div><div style="margin:0px">Codename:<span style="white-space:pre-wrap"> </span>precise</div></div><div><br></div><div>This is perl 5, version 18, subversion 1 (v5.18.1) built for x86_64-linux-thread-multi</div>
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<br></blockquote></div><br></div>