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

[FERRARI Anthony]

I am afraid this might not be the only problem. I have now installed "homo_sapiens_refseq/85_GRCh38”
and run :


/data-ddn/software/VEP/ensembl-tools-release-85/scripts/variant_effect_predictor/variant_effect_predictor.pl \
--force_overwrite \
--refseq \
--fork 4 \
--buffer_size 50000 \
--dir ensembl-tools-release-85/scripts/variant_effect_predictor/cache \
--cache \
--offline \
--no_stats \
--species homo_sapiens \
--assembly GRCh38 \
--fasta /references/human_g1k_v38.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 \
--vcf \
--output_file out.vcf


The APPRIS data is still missing/not used.
I have attached the sample VCFs to reproduce the test. There are only 3 lines.

For instance in the first line (gene ZBBX), the annotation block selected is the one for NM_001199201.1
whereas this should be the one for NM_024687.3 if we refer to this webpage : http://appris.bioinfo.cnio.es/#/database/id/homo_sapiens/79740?as=hg38&sc=refseq

Moreover the —appris flag produces no data in the VCF.


Best regards,
Anthony



On 11 Aug 2016, at 17:33, Will McLaren <wm2 at ebi.ac.uk<mailto:wm2 at ebi.ac.uk>> wrote:

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<mailto: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<http://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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