<div dir="ltr">Dear Andrew,<div><br></div><div>Thanks for reporting this; the code was mistakenly sorting biotypes in the opposite direction than intended.</div><div><br></div><div>I have pushed a fix to GitHub for this; if you re-run INSTALL.pl it should pick up the new code for you (or do a git pull in ensembl-variation if you retrieved the API code from GitHub yourself).</div>
<div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 19 March 2014 21:05, Andrew Carson <span dir="ltr"><<a href="mailto:acarson@invivoscribe.com" target="_blank">acarson@invivoscribe.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div lang="EN-US" link="blue" vlink="purple"><div><p class="MsoNormal">Hi,<u></u><u></u></p><p class="MsoNormal">I’m having an issue with the --pick filtering option using the <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> script (version 75). For a certain variant (see below), it is unclear why this filter is “picking” the specified consequence over seemingly higher ranked consequences.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Here is the variant in .vcf format:<u></u><u></u></p><p class="MsoNormal">19 33793007 . TCGC T . PASS<u></u><u></u></p><p class="MsoNormal">
<u></u> <u></u></p><p class="MsoNormal">The unfiltered/unpicked consequence is as follows:<u></u><u></u></p><p class="MsoNormal">CSQ=-|ENSG00000245848|ENST00000498907|Transcript|inframe_deletion|461-463|311-313|104-105|GD/D|gGCGac/gac|COSM18270&TMP_ESP_19_33793008_33793010||||||||-1||YES|CEBPA|HGNC||||protein_coding|Low_complexity_(Seg):Seg&PROSITE_profiles:PS50315&PIRSF_domain:PIRSF005879|CCDS54243.1|ENST00000498907.2:c.311_313delGCG|ENSP00000427514.1:p.Gly104del|||||,-|ENSG00000267130|ENST00000593041|Transcript|upstream_gene_variant||||||COSM18270&TMP_ESP_19_33793008_33793010|||||||2932|1||YES|CTD-2540B15.9|Clone_based_vega_gene||||lincRNA|||||||||,-|ENSG00000267727|ENST00000587312|Transcript|downstream_gene_variant||||||COSM18270&TMP_ESP_19_33793008_33793010|||||||162|1||YES|CTD-2540B15.7|Clone_based_vega_gene||||antisense|||||||||,-|ENSG00000178863|ENST00000320232|Transcript|upstream_gene_variant||||||COSM18270&TMP_ESP_19_33793008_33793010|||||||966|1||YES|CEBPA-AS1|HGNC||||pseudogene|||||||||,-|ENSG00000267580|ENST00000589932|Transcript|downstream_gene_variant||||||COSM18270&TMP_ESP_19_33793008_33793010|||||||934|1||YES|CTD-2540B15.11|Clone_based_vega_gene||||antisense|||||||||,-|ENSG00000267296|ENST00000592982|Transcript|upstream_gene_variant||||||COSM18270&TMP_ESP_19_33793008_33793010|||||||753|1||YES|CEBPA-AS1|Clone_based_vega_gene||||antisense|||||||||,-|ENSG00000230259|ENST00000425420|Transcript|intron_variant&nc_transcript_variant&feature_truncation||||||COSM18270&TMP_ESP_19_33793008_33793010||||||||-1||YES|AC008738.1|Clone_based_ensembl_gene||||pseudogene|||ENST00000425420.2:n.246+175_246+177delGCG||||||,-||ENSR00000345628|RegulatoryFeature|regulatory_region_variant||||||COSM18270&TMP_ESP_19_33793008_33793010|||||||||||||||||||||||||<u></u><u></u></p>
<p class="MsoNormal"><br>Although hard to see, the first consequence is inframe_deletion of a protein_coding transcript. This seems to be the consequence that should be highest ranked. However, when I use --pick, I get the following consequence:<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">CSQ=-|ENSG00000230259|ENST00000425420|Transcript|intron_variant&nc_transcript_variant&feature_truncation||||||COSM18270&TMP_ESP_19_33793008_33793010||||||||-1||YES|AC008738.1|Clone_based_ensembl_gene||||pseudogene|||ENST00000425420.2:n.246+175_246+177delGCG||||||<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">This is an intron_variant&nc_transcript_variant&feature_truncation of a pseudogene. I believe this should be of lower rank based on biotype and consequence type. <u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Is there a reason why the --pick filter is choosing this consequence over other (seemingly more relevant) consequences? Is it because there are multiple consequences (intron_variant + nc_transcript_variant + feature_truncation) in the same consequence?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Note, when I run this same variant through the VEP Web interface, I get the same consequence when selecting “Show one selected consequence per variant”.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Any help would be greatly appreciated!<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal"><span style="font-family:"Myriad Pro","sans-serif"">Andrew R. Carson, Ph.D.</span> <u></u><u></u></p>
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<br></blockquote></div><br></div>