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

Matteo matteodeg at gmail.com
Fri Feb 26 10:06:39 GMT 2016 

oh, so that's the reason... Even if I use an older version of VEP ?
Are you going to update dbNSFP for GRCh37 in the future?

Thank you,

Matteo

Il 26/02/2016 10:59, Will McLaren ha scritto:
> 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 
> <mailto: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
>     <http://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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