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Hi Will,<br>
<br>
And thank you for your response. I'll wait for the solution. I like
the idea that you can incorporate your own data to run VEP.<br>
<br>
Thanks,<br>
Heidi Viitaniemi<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">19.3.2013 13:42, Will McLaren
kirjoitti:<br>
</div>
<blockquote
cite="mid:CAMVEDX0FqZs3tRVrJuPC90tcAg1pfSYvKG+ViedYxmHBz0jhfg@mail.gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<div dir="ltr">Hello Heidi,
<div><br>
</div>
<div style="">Thanks for finding this - the causes of this bug
are I believe somewhat complex so may take a while to get to
the bottom of it.</div>
<div style=""><br>
</div>
<div style="">Just wanted to let you know that your mail is not
being ignored!</div>
<div style=""><br>
</div>
<div style="">Regards</div>
<div style=""><br>
</div>
<div style="">Will McLaren</div>
<div style="">Ensembl Variation</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 18 March 2013 13:48, Heidi
Viitaniemi <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:hmviit@utu.fi" target="_blank">hmviit@utu.fi</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> Hi,<br>
<br>
I'm running version 2.7 on a unix server. I want to create
a custom cache using my own gtf and fasta with <a
moz-do-not-send="true" href="http://gtf2vep.pl"
target="_blank">gtf2vep.pl</a>. This works without
problem and also running VEP seems to go fine. The problem
is that, in the output it seems that the cDNA_position,
CDS_position and Protein_position are correct given my
input gtf file but the calls for Amino_acids and Codons
seem completely random. If I run against the cache
retrieved from ensembl these are all correct. The version
of the genome didn't have an effect on the output, the
gtf's haven't changed. The gtf and the fasta that I'm
using for the custom originate from the ensembl reference
so I don't see any reason why the custom cache shouldn't
perform the same way as the reference from ensembl cache.
Could there be bug that somehow messes up the link between
the custom gtf and fasta in my run? Below are the commands
I ran and a snippet of the output's I got.<br>
<br>
Thanks,<br>
Heidi Viitaniemi<br>
<br>
For custom cache I'm running (wrong output for Amino_acids
and Codons)<br>
perl <a moz-do-not-send="true" href="http://gtf2vep.pl"
target="_blank">gtf2vep.pl</a> -i
GasAcu1.67_group_xixflip.gtf -f
gasAcu_group_withoutbac_inv7.fa -d 67 -s
Gasterosteus_aculeatus_XIXflipped_18032013<br>
perl <a moz-do-not-send="true"
href="http://variant_effect_predictor.pl"
target="_blank">variant_effect_predictor.pl</a> -offline
1 -dir $HOME/.vep -i ens_realigned_AK_F.var.vcf -format
vcf -fork 4 -db_version 67 -species
Gasterosteus_aculeatus_XIXflipped_18032013 -numbers
-per_gene -buffer_size 10000 -o
VEP_18032013_exon_pergene_AK_F.var.vcf.txt<br>
<br>
<table style="border-collapse:collapse" height="89"
width="1587" border="0" cellpadding="0" cellspacing="0">
<colgroup><col style="width:125pt" width="167"> <col
style="width:119pt" width="158"> <col
style="width:48pt" width="64"> <col
style="width:136pt" width="181"> <col
style="width:118pt" width="157"> <col
style="width:68pt" width="90"> <col
style="width:136pt" width="181"> <col
style="width:85pt" span="2" width="113"> <col
style="width:48pt" span="6" width="64"> <col
style="width:136pt" width="181"> </colgroup><tbody>
<tr style="min-height:15.0pt" height="20">
<td style="min-height:15.0pt;width:125pt"
height="20" width="167">groupXIX_2822477_C/T</td>
<td style="width:119pt" width="158">groupXIX:2822477</td>
<td style="width:48pt" width="64">T</td>
<td style="width:136pt" width="181">ENSGACG00000003129</td>
<td style="width:118pt" width="157">ENSGACT00000004109</td>
<td style="width:68pt" width="90">Transcript</td>
<td style="width:136pt" width="181">missense_variant</td>
<td style="width:48pt" width="64" align="right">67</td>
<td style="width:48pt" width="64" align="right">49</td>
<td style="width:48pt" width="64" align="right">17</td>
<td style="width:48pt" width="64">G/R</td>
<td style="width:48pt" width="64">Gga/Aga</td>
<td style="width:48pt" width="64">-</td>
<td style="width:136pt" width="181">EXON=1/2</td>
</tr>
<tr style="min-height:15.0pt" height="20">
<td style="min-height:15.0pt" height="20">groupXIX_2822500_T/C</td>
<td>groupXIX:2822500</td>
<td>C</td>
<td>ENSGACG00000003129</td>
<td>ENSGACT00000004109</td>
<td>Transcript</td>
<td>missense_variant</td>
<td align="right">44</td>
<td align="right">26</td>
<td align="right">9</td>
<td>Y/C</td>
<td>tAt/tGt</td>
<td>-</td>
<td>EXON=1/2</td>
</tr>
<tr style="min-height:15.0pt" height="20">
<td style="min-height:15.0pt" height="20">groupXIX_2822523_C/T</td>
<td>groupXIX:2822523</td>
<td>T</td>
<td>ENSGACG00000003129</td>
<td>ENSGACT00000004109</td>
<td>Transcript</td>
<td>synonymous_variant</td>
<td align="right">21</td>
<td align="right">3</td>
<td align="right">1</td>
<td>R</td>
<td>cgG/cgA</td>
<td>-</td>
<td>EXON=1/2</td>
</tr>
<tr style="min-height:15.0pt" height="20">
<td style="min-height:15.0pt" height="20">groupXIX_2822541_T/A</td>
<td>groupXIX:2822541</td>
<td>A</td>
<td>ENSGACG00000003129</td>
<td>ENSGACT00000004109</td>
<td>Transcript</td>
<td>5_prime_UTR_variant</td>
<td align="right">3</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>EXON=1/2</td>
</tr>
</tbody>
</table>
<br>
<br>
For ensembl cache I'm running (correct output for
Amino_acids and Codons)<br>
perl <a moz-do-not-send="true"
href="http://variant_effect_predictor.pl"
target="_blank">variant_effect_predictor.pl</a> -offline
-dir $HOME/.vep -i ens_realigned_AK_F.var.vcf -format vcf
-fork 4 -db_version 69 -species gasterosteus_aculeatus
-numbers -per_gene -buffer_size 10000 -o
ensVEP_18032013_exon_pergene_AK_F.var.vcf.txt<br>
<br>
<span class="HOEnZb"><font color="#888888"> </font></span><span
class="HOEnZb"><font color="#888888"> </font></span><span
class="HOEnZb"><font color="#888888"> </font></span>
<table style="border-collapse:collapse;width:1101pt"
width="1468" border="0" cellpadding="0" cellspacing="0">
<colgroup><col style="width:122pt" width="163"> <col
style="width:92pt" width="122"> <col
style="width:48pt" width="64"> <col
style="width:109pt" width="145"> <col
style="width:107pt" width="143"> <col
style="width:117pt" width="156"> <col
style="width:170pt" width="227"> <col
style="width:48pt" span="7" width="64"> </colgroup><tbody>
<tr style="min-height:15.0pt" height="20">
<td style="min-height:15.0pt;width:122pt"
height="20" width="163">groupXIX_2822477_C/T</td>
<td style="width:92pt" width="122">groupXIX:2822477</td>
<td style="width:48pt" width="64">T</td>
<td style="width:109pt" width="145">ENSGACG00000003129</td>
<td style="width:107pt" width="143">ENSGACT00000004109</td>
<td style="width:117pt" width="156">Transcript</td>
<td style="width:170pt" width="227">missense_variant</td>
<td style="width:48pt" width="64" align="right">67</td>
<td style="width:48pt" width="64" align="right">49</td>
<td style="width:48pt" width="64" align="right">17</td>
<td style="width:48pt" width="64">A/T</td>
<td style="width:48pt" width="64">Gcg/Acg</td>
<td style="width:48pt" width="64">-</td>
<td style="width:48pt" width="64">EXON=1/2</td>
</tr>
<tr style="min-height:15.0pt" height="20">
<td style="min-height:15.0pt" height="20">groupXIX_2822500_T/C</td>
<td>groupXIX:2822500</td>
<td>C</td>
<td>ENSGACG00000003129</td>
<td>ENSGACT00000004109</td>
<td>Transcript</td>
<td>missense_variant</td>
<td align="right">44</td>
<td align="right">26</td>
<td align="right">9</td>
<td>D/G</td>
<td>gAc/gGc</td>
<td>-</td>
<td>EXON=1/2</td>
</tr>
<tr style="min-height:15.0pt" height="20">
<td style="min-height:15.0pt" height="20">groupXIX_2822523_C/T</td>
<td>groupXIX:2822523</td>
<td>T</td>
<td>ENSGACG00000003129</td>
<td>ENSGACT00000004109</td>
<td>Transcript</td>
<td>initiator_codon_variant</td>
<td align="right">21</td>
<td align="right">3</td>
<td align="right">1</td>
<td>M/I</td>
<td>atG/atA</td>
<td>-</td>
<td>EXON=1/2</td>
</tr>
<tr style="min-height:15.0pt" height="20">
<td style="min-height:15.0pt" height="20">groupXIX_2822541_T/A</td>
<td>groupXIX:2822541</td>
<td>A</td>
<td>ENSGACG00000003129</td>
<td>ENSGACT00000004109</td>
<td>Transcript</td>
<td>5_prime_UTR_variant</td>
<td align="right">3</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>EXON=1/2</td>
</tr>
</tbody>
</table>
<span class="HOEnZb"><font color="#888888"> <br>
<br>
<pre cols="72">--
______________________________________________
Heidi Viitaniemi
PhD student
Division of Genetics and Physiology
Department of Biology
Itäinen Pitkäkatu 4A, 7th floor (Pharmacity)
University of Turku
20520 Turku
FINLAND </pre>
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<pre class="moz-signature" cols="72">--
______________________________________________
Heidi Viitaniemi
PhD student
Division of Genetics and Physiology
Department of Biology
Itäinen Pitkäkatu 4A, 7th floor (Pharmacity)
University of Turku
20520 Turku
FINLAND </pre>
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