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

Fri Feb 26 10:31:06 GMT 2016

Apologies, I've just checked the dbNSFP website and it appears you can
download older versions of dbNSFP which are compatible with hg19/GRCh37.

It's hard to tell from the documentation, but it looks like the dbNSFP
v2.6 (July
26, 2014) release was the last to contain GRCh37 as the primary position.
This in theory should work out of the box with the VEP plugin.

https://sites.google.com/site/jpopgen/dbNSFP

Regards

Will

On 26 February 2016 at 10:19, Will McLaren <wm2 at ebi.ac.uk> wrote:

> We at Ensembl do not produce the dbNSFP database, just a plugin to access
> it.
>
> The dbNSFP file does actually contain position mappings to GRCh37, but
> using this as the index would generate many artefacts in the results due to
> differences in genome and transcript structure. In theory it would be
> possible to modify the plugin to do this, but the major task would be
> re-ordering and re-indexing the data files (tabix requires that the file be
> sorted by the position column that it will index).
>
> HTH
>
> Will
>
> On 26 February 2016 at 10:06, Matteo <matteodeg at gmail.com> wrote:
>
>> 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> 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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>>
>>
>>
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