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<div class="">OK thank you Will. I have run the same small exemple with GRCh38 then.</div>
<div class="">For the first position here is what I obtain (I removed some cols for readability) :</div>
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<div class="">cache = homo_sapiens/85_GRCh38</div>
<div class="">position (GRCh38) = 3:167266887</div>
<div class="">—pick_order = appris,tsl,ccds,biotype</div>
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<div class="">Allele | SYMBOL | Gene | Feature | HGVSc | PICK | TSL | APPRIS | RefSeq</div>
<div class="">A|ZBBX|ENSG00000169064|ENST00000307529|ENST00000307529.9:c.2254+15351C>T|1|1|A2|</div>
<div class="">A|ZBBX|ENSG00000169064|ENST00000392764|ENST00000392764.5:c.2050+15351C>T||5|A2|NM_001199202.1</div>
<div class="">A|ZBBX|ENSG00000169064|ENST00000392766|ENST00000392766.6:c.2137+15351C>T||2|P3|NM_024687.3||||||</div>
<div class="">A|ZBBX|ENSG00000169064|ENST00000392767|ENST00000392767.6:c.2050+15351C>T||1|A2|</div>
<div class="">A|ZBBX|ENSG00000169064|ENST00000455345|ENST00000455345.6:c.2254+15351C>T||1|A2|NM_001199201.1</div>
<div class="">A|ZBBX|ENSG00000169064|ENST00000464922|ENST00000464922.5:c.85-14676C>T||3||</div>
<div class="">A|ZBBX|ENSG00000169064|ENST00000465071|ENST00000465071.1:n.335+15351C>T||2||</div>
<div class="">A|ZBBX|ENSG00000169064|ENST00000492642|ENST00000492642.5:c.222+15351C>T||5||</div>
<div class="">A|ZBBX|ENSG00000169064|ENST00000494898|ENST00000494898.5:c.*70-14676C>T||2||</div>
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<div class="">So, the chosen transcript is the first one which is an APPRIS “alternative2”. The third transcript is a “principal3”</div>
<div class="">and (I suppose, if I correctly understood APPRIS system) should be chosen. </div>
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<div class="">In VEP.pm, there is this block :</div>
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<div class=""> if(my ($appris) = @{$tr->get_all_Attributes('appris')}) {</div>
<div class=""> if($appris->value =~ m/([A-Za-z])(\d+)/) {</div>
<div class=""> my ($type, $grade) = ($1, $2);</div>
<div class=""> # values are principal1, principal2, ..., alternative1, alternative2</div>
<div class=""> # so add 10 to grade if alternate</div>
<div class=""> $grade += 10 if substr($type, 0, 1) eq 'a';</div>
<div class=""> $info->{appris} = $grade if $grade;</div>
<div class=""> }</div>
<div class=""> }</div>
<div class=""> }</div>
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<div class="">The regex pattern $appris->value =~ m/([A-Za-z])(\d+)/ should be changed to $appris->value =~ m/([A-Za-z]+)(\d+)/</div>
<div class="">or it only selects the last letter from the word ‘alternative’/‘principal’ and you never get something equal to ‘a’ when you</div>
<div class="">try to modify $grade for ‘alternative' values. At the end, the selected transcript is the one with the smallest number</div>
<div class="">regardless of being 'principal' or 'alternate’.</div>
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<div class="">Best wishes,</div>
<div class="">Anthony</div>
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<blockquote type="cite" class="">
<div class="">On 11 Aug 2016, at 19:45, Will McLaren <<a href="mailto:wm2@ebi.ac.uk" class="">wm2@ebi.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<p dir="ltr" class="">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" class="">Regards</p>
<p dir="ltr" class="">Will</p>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On 11 Aug 2016 17:28, "FERRARI Anthony" <<a href="mailto:anthony.ferrari@lyon.unicancer.fr" class="">anthony.ferrari@lyon.unicancer.fr</a>> wrote:<br type="attribution" class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="">
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<div class="">I am afraid this might not be the only problem. I have now installed "homo_sapiens_refseq/85_<wbr class="">GRCh38”</div>
<div class="">and run :</div>
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<div class="">
<div class="">/data-ddn/software/VEP/<wbr class="">ensembl-tools-release-85/<wbr class="">scripts/variant_effect_<wbr class="">predictor/<a href="http://variant_effect_predictor.pl/" target="_blank" class="">variant_effect_<wbr class="">predictor.pl</a> \</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/<wbr class="">scripts/variant_effect_<wbr class="">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.<wbr class="">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>
</div>
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</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>
<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" target="_blank" class="">
http://appris.bioinfo.cnio.es/<wbr class="">#/database/id/homo_sapiens/<wbr class="">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" target="_blank" class="">wm2@ebi.ac.uk</a>> wrote:</div>
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<div class="">
<div dir="ltr" class="">Hi Anthony,
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</div>
<div class="">APPRIS is not available on GRCh37, I'm afraid, only GRCh38 for human.</div>
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</div>
<div class="">Regards</div>
<div class=""><br class="">
</div>
<div class="">Will McLaren</div>
<div class="">Ensembl Variation</div>
</div>
<div class=""><br class="">
<div class="">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.<wbr class="">unicancer.fr</a>></span> wrote:<br class="">
<blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex" class="">
<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_GRCh37<wbr class="">).<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.fast<wbr class="">a \<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('app<wbr class="">ris')}) {<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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