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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 gtf2vep.pl. 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 gtf2vep.pl -i GasAcu1.67_group_xixflip.gtf -f
gasAcu_group_withoutbac_inv7.fa -d 67 -s
Gasterosteus_aculeatus_XIXflipped_18032013<br>
perl variant_effect_predictor.pl -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;" width="1587" border="0"
cellpadding="0" cellspacing="0" height="89">
<colgroup><col
style="mso-width-source:userset;mso-width-alt:6107;width:125pt"
width="167"> <col
style="mso-width-source:userset;mso-width-alt:5778;width:119pt"
width="158"> <col style="width:48pt" width="64"> <col
style="mso-width-source:userset;mso-width-alt:6619;width:136pt"
width="181"> <col
style="mso-width-source:userset;mso-width-alt:5741;width:118pt"
width="157"> <col
style="mso-width-source:userset;mso-width-alt:3291;width:68pt"
width="90"> <col
style="mso-width-source:userset;mso-width-alt:6619;width:136pt"
width="181"> <col
style="mso-width-source:userset;mso-width-alt:4132;
width:85pt" span="2" width="113"> <col style="width:48pt"
span="6" width="64"> <col
style="mso-width-source:userset;mso-width-alt:6619;width:136pt"
width="181"> </colgroup><tbody>
<tr style="height:15.0pt" height="20">
<td style="height:15.0pt;width:125pt" width="167" height="20">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="height:15.0pt" height="20">
<td style="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="height:15.0pt" height="20">
<td style="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="height:15.0pt" height="20">
<td style="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 variant_effect_predictor.pl -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>
<table style="border-collapse: collapse;width:1101pt" width="1468"
border="0" cellpadding="0" cellspacing="0">
<colgroup><col
style="mso-width-source:userset;mso-width-alt:5961;width:122pt"
width="163"> <col
style="mso-width-source:userset;mso-width-alt:4461;width:92pt"
width="122"> <col style="width:48pt" width="64"> <col
style="mso-width-source:userset;mso-width-alt:5302;width:109pt"
width="145"> <col
style="mso-width-source:userset;mso-width-alt:5229;width:107pt"
width="143"> <col
style="mso-width-source:userset;mso-width-alt:5705;width:117pt"
width="156"> <col
style="mso-width-source:userset;mso-width-alt:8301;width:170pt"
width="227"> <col style="width:48pt" span="7" width="64"> </colgroup><tbody>
<tr style="height:15.0pt" height="20">
<td style="height:15.0pt;width:122pt" width="163" height="20">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="height:15.0pt" height="20">
<td style="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="height:15.0pt" height="20">
<td style="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="height:15.0pt" height="20">
<td style="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>
<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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