<p dir="ltr">Apologies, I should have been clearer, Appris is available only for Ensembl transcripts on GRCh38. It is not available for RefSeq transcripts on any assembly.</p>
<p dir="ltr">Regards</p>
<p dir="ltr">Will</p>
<div class="gmail_extra"><br><div class="gmail_quote">On 11 Aug 2016 17:28, "FERRARI Anthony" <<a href="mailto:anthony.ferrari@lyon.unicancer.fr">anthony.ferrari@lyon.unicancer.fr</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="word-wrap:break-word">
<div><br>
</div>
<div>I am afraid this might not be the only problem. I have now installed "homo_sapiens_refseq/85_<wbr>GRCh38”</div>
<div>and run :</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>/data-ddn/software/VEP/<wbr>ensembl-tools-release-85/<wbr>scripts/variant_effect_<wbr>predictor/<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_<wbr>predictor.pl</a> \</div>
<div>--force_overwrite \</div>
<div>--refseq \</div>
<div>--fork 4 \</div>
<div>--buffer_size 50000 \</div>
<div>--dir ensembl-tools-release-85/<wbr>scripts/variant_effect_<wbr>predictor/cache \</div>
<div>--cache \</div>
<div>--offline \</div>
<div>--no_stats \</div>
<div>--species homo_sapiens \</div>
<div>--assembly GRCh38 \</div>
<div>--fasta /references/human_g1k_v38.<wbr>fasta \</div>
<div>--variant_class \</div>
<div>--canonical \</div>
<div>--polyphen b --sift b \</div>
<div>--total_length \</div>
<div>--numbers \</div>
<div>--hgvs \</div>
<div>--appris \</div>
<div>--protein \</div>
<div>--symbol \</div>
<div>--biotype \</div>
<div>--check_existing \</div>
<div>--pick_order refseq,appris,tsl,ccds,biotype \</div>
<div>--flag_pick \</div>
<div>--format vcf \</div>
<div>--input_file input.vcf \</div>
<div>--vcf \</div>
<div>--output_file out.vcf</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>The APPRIS data is still missing/not used.</div>
<div>I have attached the sample VCFs to reproduce the test. There are only 3 lines.</div>
<div><br>
</div>
<div>For instance in the first line (gene ZBBX), the annotation block selected is the one for NM_001199201.1</div>
<div>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" target="_blank">
http://appris.bioinfo.cnio.es/<wbr>#/database/id/homo_sapiens/<wbr>79740?as=hg38&sc=refseq</a></div>
<div><br>
</div>
<div>Moreover the —appris flag produces no data in the VCF.</div>
<div><br>
</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Anthony</div>
<div><br>
</div>
<div></div>
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<div></div>
<div><br>
</div>
<br>
<div>
<blockquote type="cite">
<div>On 11 Aug 2016, at 17:33, Will McLaren <<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>> wrote:</div>
<br>
<div>
<div dir="ltr">Hi Anthony,
<div><br>
</div>
<div>APPRIS is not available on GRCh37, I'm afraid, only GRCh38 for human.</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
</div>
<div><br>
<div>On 11 August 2016 at 16:20, FERRARI Anthony <span dir="ltr">
<<a href="mailto:anthony.ferrari@lyon.unicancer.fr" target="_blank">anthony.ferrari@lyon.<wbr>unicancer.fr</a>></span> wrote:<br>
<blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Hi,<br>
<br>
I am using the VEP script to annotate whole-genome SNVs. I have just installed the version 85 with<br>
the INSTALL.pl script and built the cache for refseq/GRCh37 (homo_sapiens_refseq/85_GRCh37<wbr>).<br>
<br>
I use the following command to launch the analysis :<br>
<br>
variant_effect_predictor/<a href="http://variant_effect_predictor.pl/" rel="noreferrer" target="_blank">varia<wbr>nt_effect_predictor.pl</a> \<br>
--refseq \<br>
--fork 4 \<br>
--buffer_size 50000 \<br>
--dir variant_effect_predictor/cache \<br>
--cache \<br>
--offline \<br>
--no_stats \<br>
--fasta /references/human_g1k_v37.fast<wbr>a \<br>
--variant_class \<br>
--canonical \<br>
--polyphen b --sift b \<br>
--total_length \<br>
--numbers \<br>
--hgvs \<br>
--appris \<br>
--protein \<br>
--symbol \<br>
--biotype \<br>
--check_existing \<br>
--pick_order refseq,appris,tsl,ccds,biotype \<br>
--flag_pick \<br>
--format vcf \<br>
--input_file ${INPUT} \<br>
--vcf \<br>
--output_file ${OUTPUT}<br>
<br>
<br>
So basically I would like to flag, whenever possible, the annotation block with APPRIS principal<br>
isoform. In the VEP.pm module, I have inserted a few “print" statement in the "pick_worst_vfoa"<br>
function. It looks like I never get into this if block (line 2291) :<br>
<br>
if(my ($appris) = @{$tr->get_all_Attributes('app<wbr>ris')}) {<br>
...<br>
}<br>
<br>
and the $info->{appris} is always “100”, its default value.<br>
<br>
APPRIS does not have any influence on the flag_pick process.<br>
Do I need to install some other DB/file for VEP to be able to get to the APPRIS info ?<br>
(Is it an —offline or GRCh37 thing ?)<br>
<br>
<br>
Many thanks for your help,<br>
Anthony<br>
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<br>
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</blockquote>
</div>
<br>
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<br></blockquote></div></div>