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

[FERRARI Anthony]

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