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oh, so that's the reason... Even if I use an older version of VEP ?
<br>
Are you going to update dbNSFP for GRCh37 in the future?<br>
<br>
Thank you,<br>
<br>
Matteo<br>
<br>
<div class="moz-cite-prefix">Il 26/02/2016 10:59, Will McLaren ha
scritto:<br>
</div>
<blockquote
cite="mid:CAMVEDX1+=b9KpmuDiiqeh-1hJCf+5vwhg-zMYLXoU_WX9QBwZA@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Mateo,
<div><br>
</div>
<div>The dbNSFP plugin is currently compatible only with GRCh38.</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 26 February 2016 at 09:45, Matteo <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:matteodeg@gmail.com" target="_blank">matteodeg@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Hi all,<br>
<br>
I'm using vep tool to annotate variants and this is my
command line:<br>
<br>
perl <a moz-do-not-send="true"
href="http://variant_effect_predictor.pl" rel="noreferrer"
target="_blank">variant_effect_predictor.pl</a> -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<br>
<br>
My vep release is the last one (83) and I'm using GRCH37 but
i get the following error from dbNSFP:<br>
<br>
Use of uninitialized value $2 in concatenation (.) or string
at /home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM>
line 3.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM>
line 3.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 4.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 5.<br>
Use of uninitialized value $2 in concatenation (.) or string
at /home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM>
line 6.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM>
line 6.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 7.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 8.<br>
Use of uninitialized value $2 in concatenation (.) or string
at /home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM>
line 9.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM>
line 9.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 10.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 11.<br>
Use of uninitialized value $2 in concatenation (.) or string
at /home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM>
line 12.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM>
line 12.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 13.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 14.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 15.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 16.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 17.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 18.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 19.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 20.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 21.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 22.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 23.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 24.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 25.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 26.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 27.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 28.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 29.<br>
Use of uninitialized value $2 in concatenation (.) or string
at /home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM>
line 30.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM>
line 30.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 31.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 32.<br>
Use of uninitialized value $2 in concatenation (.) or string
at /home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM>
line 33.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM>
line 33.<br>
Use of uninitialized value $col in hash element at
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM>
line 34.<br>
.<br>
.<br>
.<br>
and so on<br>
<br>
In my output file, some variants have been annotated only
with clinvar. Do you have any idea?<br>
Thank you in advice for your help,<br>
<br>
Matteo<br>
<br>
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</blockquote>
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