<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><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 class="Apple-tab-span" style="white-space:pre"> </span>93528-38598955</div><div style="margin: 0px;">9<span class="Apple-tab-span" style="white-space: pre;"> </span>139308932-141071552</div><div style="margin: 0px;"><div style="margin: 0px;">10<span class="Apple-tab-span" style="white-space:pre"> </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/variant_effect_predictor.pl -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 class="Apple-tab-span" style="white-space:pre"> </span>Ubuntu</div><div style="margin: 0px;">Description:<span class="Apple-tab-span" style="white-space:pre"> </span>Ubuntu 12.04.2 LTS</div><div style="margin: 0px;">Release:<span class="Apple-tab-span" style="white-space:pre"> </span>12.04</div><div style="margin: 0px;">Codename:<span class="Apple-tab-span" style="white-space:pre"> </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></div><div><br></div></body></html>