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<div class="">I am afraid this might not be the only problem. I have now installed "homo_sapiens_refseq/85_GRCh38”</div>
<div class="">and run :</div>
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</div>
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<div class="">
<div class="">/data-ddn/software/VEP/ensembl-tools-release-85/scripts/variant_effect_predictor/variant_effect_predictor.pl \</div>
<div class="">--force_overwrite \</div>
<div class="">--refseq \</div>
<div class="">--fork 4 \</div>
<div class="">--buffer_size 50000 \</div>
<div class="">--dir ensembl-tools-release-85/scripts/variant_effect_predictor/cache \</div>
<div class="">--cache \</div>
<div class="">--offline \</div>
<div class="">--no_stats \</div>
<div class="">--species homo_sapiens \</div>
<div class="">--assembly GRCh38 \</div>
<div class="">--fasta /references/human_g1k_v38.fasta \</div>
<div class="">--variant_class \</div>
<div class="">--canonical \</div>
<div class="">--polyphen b --sift b \</div>
<div class="">--total_length \</div>
<div class="">--numbers \</div>
<div class="">--hgvs \</div>
<div class="">--appris \</div>
<div class="">--protein \</div>
<div class="">--symbol \</div>
<div class="">--biotype \</div>
<div class="">--check_existing \</div>
<div class="">--pick_order refseq,appris,tsl,ccds,biotype \</div>
<div class="">--flag_pick \</div>
<div class="">--format vcf \</div>
<div class="">--input_file input.vcf \</div>
<div class="">--vcf \</div>
<div class="">--output_file out.vcf</div>
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<div class="">The APPRIS data is still missing/not used.</div>
<div class="">I have attached the sample VCFs to reproduce the test. There are only 3 lines.</div>
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<div class="">For instance in the first line (gene ZBBX), the annotation block selected is the one for NM_001199201.1</div>
<div class="">whereas this should be the one for NM_024687.3 if we refer to this webpage :
<a href="http://appris.bioinfo.cnio.es/#/database/id/homo_sapiens/79740?as=hg38&sc=refseq" class="">
http://appris.bioinfo.cnio.es/#/database/id/homo_sapiens/79740?as=hg38&sc=refseq</a></div>
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<div class="">Moreover the —appris flag produces no data in the VCF.</div>
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<div class="">Best regards,</div>
<div class="">Anthony</div>
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<blockquote type="cite" class="">
<div class="">On 11 Aug 2016, at 17:33, Will McLaren <<a href="mailto:wm2@ebi.ac.uk" class="">wm2@ebi.ac.uk</a>> wrote:</div>
<br class="x_Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hi Anthony,
<div class=""><br class="">
</div>
<div class="">APPRIS is not available on GRCh37, I'm afraid, only GRCh38 for human.</div>
<div class=""><br class="">
</div>
<div class="">Regards</div>
<div class=""><br class="">
</div>
<div class="">Will McLaren</div>
<div class="">Ensembl Variation</div>
</div>
<div class="x_gmail_extra"><br class="">
<div class="x_gmail_quote">On 11 August 2016 at 16:20, FERRARI Anthony <span dir="ltr" class="">
<<a href="mailto:anthony.ferrari@lyon.unicancer.fr" target="_blank" class="">anthony.ferrari@lyon.unicancer.fr</a>></span> wrote:<br class="">
<blockquote class="x_gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<br class="">
Hi,<br class="">
<br class="">
I am using the VEP script to annotate whole-genome SNVs. I have just installed the version 85 with<br class="">
the INSTALL.pl script and built the cache for refseq/GRCh37 (homo_sapiens_refseq/85_<wbr class="">GRCh37).<br class="">
<br class="">
I use the following command to launch the analysis :<br class="">
<br class="">
variant_effect_predictor/<a href="http://variant_effect_predictor.pl/" rel="noreferrer" target="_blank" class="">varia<wbr class="">nt_effect_predictor.pl</a> \<br class="">
--refseq \<br class="">
--fork 4 \<br class="">
--buffer_size 50000 \<br class="">
--dir variant_effect_predictor/cache \<br class="">
--cache \<br class="">
--offline \<br class="">
--no_stats \<br class="">
--fasta /references/human_g1k_v37.<wbr class="">fasta \<br class="">
--variant_class \<br class="">
--canonical \<br class="">
--polyphen b --sift b \<br class="">
--total_length \<br class="">
--numbers \<br class="">
--hgvs \<br class="">
--appris \<br class="">
--protein \<br class="">
--symbol \<br class="">
--biotype \<br class="">
--check_existing \<br class="">
--pick_order refseq,appris,tsl,ccds,biotype \<br class="">
--flag_pick \<br class="">
--format vcf \<br class="">
--input_file ${INPUT} \<br class="">
--vcf \<br class="">
--output_file ${OUTPUT}<br class="">
<br class="">
<br class="">
So basically I would like to flag, whenever possible, the annotation block with APPRIS principal<br class="">
isoform. In the VEP.pm module, I have inserted a few “print" statement in the "pick_worst_vfoa"<br class="">
function. It looks like I never get into this if block (line 2291) :<br class="">
<br class="">
if(my ($appris) = @{$tr->get_all_Attributes('<wbr class="">appris')}) {<br class="">
...<br class="">
}<br class="">
<br class="">
and the $info->{appris} is always “100”, its default value.<br class="">
<br class="">
APPRIS does not have any influence on the flag_pick process.<br class="">
Do I need to install some other DB/file for VEP to be able to get to the APPRIS info ?<br class="">
(Is it an —offline or GRCh37 thing ?)<br class="">
<br class="">
<br class="">
Many thanks for your help,<br class="">
Anthony<br class="">
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