[ensembl-dev] VEP command line error using dbNSFP on GRCH37

[Will McLaren]

Hi Mateo,

The dbNSFP plugin is currently compatible only with GRCh38.

Regards

Will

On 26 February 2016 at 09:45, Matteo <matteodeg at gmail.com> wrote:

> Hi all,
>
> I'm using vep tool to annotate variants and this is my command line:
>
> perl variant_effect_predictor.pl -i ~/path/to/my.vcf -o ~/path/to/my.vcf
> --cache --vcf --assembly GRCh37 --offline --force_overwrite -v
> --variant_class --tsl --sift b --poly b --vcf_info_field ANN --hgvs
> --protein --canonical --check_existing --gmaf --pubmed --biotype
> --gene_phenotype --plugin
> dbNSFP,/path/to/ensembl-tools-release-83/dbNSFP.gz,LRT_score,LRT_pred,MutationTaster_score,MutationTaster_pred,FATHMM_score,FATHMM_pred,PROVEAN_score,PROVEAN_pred,MetaSVM_score,MetaSVM_pred,MetaLR_score,
> MetaLR_pred,clinvar_rs,clinvar_clnsig
>
> My vep release is the last one (83) and I'm using GRCH37 but i get the
> following error from dbNSFP:
>
> Use of uninitialized value $2 in concatenation (.) or string at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 3.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 3.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 4.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 5.
> Use of uninitialized value $2 in concatenation (.) or string at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 6.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 6.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 7.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 8.
> Use of uninitialized value $2 in concatenation (.) or string at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 9.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 9.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 10.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 11.
> Use of uninitialized value $2 in concatenation (.) or string at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 12.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 12.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 13.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 14.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 15.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 16.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 17.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 18.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 19.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 20.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 21.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 22.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 23.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 24.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 25.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 26.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 27.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 28.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 29.
> Use of uninitialized value $2 in concatenation (.) or string at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 30.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 30.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 31.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 32.
> Use of uninitialized value $2 in concatenation (.) or string at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 33.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 33.
> Use of uninitialized value $col in hash element at
> /home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 34.
> .
> .
> .
>  and so on
>
> In my output file, some variants have been annotated only with clinvar. Do
> you have any idea?
> Thank you in advice for your help,
>
> Matteo
>
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