[ensembl-dev] VEP "--pick_order" issue

[Will McLaren]

Hi Anthony,

APPRIS is not available on GRCh37, I'm afraid, only GRCh38 for human.

Regards

Will McLaren
Ensembl Variation

On 11 August 2016 at 16:20, FERRARI Anthony <
anthony.ferrari at lyon.unicancer.fr> wrote:

>
> Hi,
>
> I am using the VEP script to annotate whole-genome SNVs. I have just
> installed the version 85 with
> the INSTALL.pl script and built the cache for refseq/GRCh37
> (homo_sapiens_refseq/85_GRCh37).
>
> I use the following command to launch the analysis :
>
> variant_effect_predictor/variant_effect_predictor.pl \
> --refseq \
> --fork 4 \
> --buffer_size 50000 \
> --dir variant_effect_predictor/cache \
> --cache \
> --offline \
> --no_stats \
> --fasta /references/human_g1k_v37.fasta \
> --variant_class \
> --canonical \
> --polyphen b --sift b \
> --total_length \
> --numbers \
> --hgvs \
> --appris \
> --protein \
> --symbol \
> --biotype \
> --check_existing \
> --pick_order refseq,appris,tsl,ccds,biotype \
> --flag_pick \
> --format vcf \
> --input_file ${INPUT} \
> --vcf \
> --output_file ${OUTPUT}
>
>
> So basically I would like to flag, whenever possible, the annotation block
> with APPRIS principal
> isoform. In the VEP.pm module, I have inserted a few “print" statement in
> the "pick_worst_vfoa"
> function. It looks like I never get into this if block (line 2291) :
>
>      if(my ($appris) = @{$tr->get_all_Attributes('appris')}) {
> ...
>      }
>
> and the $info->{appris} is always “100”, its default value.
>
> APPRIS does not have any influence on the flag_pick process.
> Do I need to install some other DB/file for VEP to be able to get to the
> APPRIS info ?
> (Is it an —offline or GRCh37 thing ?)
>
>
> Many thanks for your help,
> Anthony
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