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<p class="MsoNormal"><span style="font-size:11.0pt">Hello,<br>
<br>
I have been using the --per_gene option in VEP to get only the most severe consequence of each gene in the CSQ field for my files (as given in the documentation here http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_per_gene). However,
I noticed something going awry today. I was checking all the consequences of a particular position in a gene (BAP1). When I give the --per_gene option in vep, it returns a single consequence for the variant and the consequence is an intron variant. When I
don’t give the –per_gene option, it returns all the possible consequences for BAP1, which includes both a missense variant and an intron variant. For some reason, the missense variant is not being reported over the intron variant while using the –per_gene
option. I ran this on build 84. The commands I used were as follows:-<br>
<br>
Using per_gene :<br>
<br>
perl /software/vertres/bin-external/variant_effect_predictor_v84.pl --offline --vcf --dir_cache /lustre/scratch116/vr/ref/ensembl/vep_cache --species homo_sapiens --assembly GRCh38 --no_progress --everything --cache --per_gene -i bap1_pos_test.vcf -o bap1_84_per_gene.vcf<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><br>
Without per_gene : <br>
<br>
perl /software/vertres/bin-external/variant_effect_predictor_v84.pl --offline --vcf --dir_cache /lustre/scratch116/vr/ref/ensembl/vep_cache --species homo_sapiens --assembly GRCh38 --no_progress --everything --cache -i bap1_pos_test.vcf -o bap1_84.vcf<br>
<br>
The output of the per_gene file doesn’t have the missense variant while the normal one does, for the same gene.
<br>
less bap1_84_per_gene.vcf | grep -c "missense"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><br>
less bap1_84.vcf | grep -c "missense"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><br>
This is contrary to what is expected from the given documentation. Could someone help clarify what is going on here ?<br>
<br>
Thanking you,<br>
Aravind<br>
<br>
<br>
<br>
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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