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

Will McLaren wm2 at ebi.ac.uk
Thu Aug 11 18:45:01 BST 2016


Apologies, I should have been clearer, Appris is available only for Ensembl
transcripts on GRCh38. It is not available for RefSeq transcripts on any
assembly.

Regards

Will

On 11 Aug 2016 17:28, "FERRARI Anthony" <anthony.ferrari at lyon.unicancer.fr>
wrote:

>
> 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> 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> 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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