[ensembl-dev] Choosing the --per_gene option in VEP

Will McLaren wm2 at ebi.ac.uk
Thu Oct 20 13:45:04 BST 2016


Hi Aravind,

The output selected is not by default based primarily on the consequence
ranking, but on the likely relevance of each affected transcript.

The default order of selection criteria is shown in the documentation [1],
and you may change this order with --pick_order if you wish to, for
example, prioritise consequence rank first.

Without having seen your input, it seems likely that your variant of
interest falls in an exon not found in the primary transcript of BAP1; if
you study the transcript diagrams [2] you can see several transcripts
contain exons (e.g. BAP1-201) that are not found in the primary transcript
as determined by CCDS, APPRIS and TSL (BAP1-001). This means it may have a
missense effect in BAP1-201 but fall in the intron of BAP1-001.

Hope that helps

Will McLaren
Ensembl Variation

[1] : http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#pick
[2] :
http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000163930;r=3:52401013-52410350

On 20 October 2016 at 13:35, Aravind Sankar <as42 at sanger.ac.uk> wrote:

> Hello,
>
> 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:-
>
> Using per_gene :
>
> 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
>
>
> Without per_gene :
>
> 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
>
> The output of the per_gene file doesn’t have the missense variant while
> the normal one does, for the same gene.
> less bap1_84_per_gene.vcf | grep -c "missense"
>
> 0
>
>
> less bap1_84.vcf | grep -c "missense"
>
> 1
>
>
> This is contrary to what is expected from the given documentation. Could
> someone help clarify what is going on here ?
>
> Thanking you,
> Aravind
>
>
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20161020/49210369/attachment.html>


More information about the Dev mailing list