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<div>Thanks so much Will! That helps explain it & I will try your suggestions.</div>
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<div>Take care,</div>
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<div>Ann</div>
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<div><font class="Apple-style-span"><font class="Apple-style-span" face="Calibri" color="#7f007f"><span class="Apple-style-span" style="font-size: 14px; ">Ann Black-Ziegelbein</span></font></font></div>
<div><font class="Apple-style-span" face="Calibri" color="#7f007f"><span class="Apple-style-span" style="font-size: 14px;">Senior Application Developer</span></font></div>
<div><span style="font-family: Calibri; "><font color="#7f007f">Molecular Otolaryngology and Renal Research Laboratories </font></span></div>
<div><span style="font-family: Calibri; "><font color="#7f007f">University of Iowa</font></span></div>
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<span style="font-weight:bold">From: </span><<a href="mailto:wmclaren@gmail.com">wmclaren@gmail.com</a>> on behalf of Will McLaren <<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>><br>
<span style="font-weight:bold">Date: </span>Monday, April 4, 2016 at 6:02 AM<br>
<span style="font-weight:bold">To: </span>Ann Black-Ziegelbein <<a href="mailto:elizabeth-black@uiowa.edu">elizabeth-black@uiowa.edu</a>><br>
<span style="font-weight:bold">Cc: </span>"<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>" <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: VEP 84 - question about output from flag_pick/pick_order<br>
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<div dir="ltr">Hi Ann,
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<div>I notice you are using the merged cache. This contains a merge of two gene sets, the one from Ensembl and the one from RefSeq. Both of these sets have, per gene, a canonical transcript assigned.</div>
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<div>The VEP has no way to determine which of these it is you would prefer to see annotated, so the canonical transcript from each of the sets are considered equal. This means the next comparator is used to split them (rank in your case), and since these will
likely be equal too, a random one is chosen.</div>
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<div>I'd suggest either using a non-merged cache (choose either Ensembl or RefSeq, or perhaps run both independently?), or add some other comparators to your --pick_order flag to help distinguish.</div>
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<div>Hope that helps.</div>
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<div>Will McLaren</div>
<div>Ensembl Variation</div>
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<div class="gmail_quote">On 1 April 2016 at 16:41, Black-Ziegelbein, Elizabeth A <span dir="ltr">
<<a href="mailto:elizabeth-black@uiowa.edu" target="_blank">elizabeth-black@uiowa.edu</a>></span> wrote:<br>
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<div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px">I am using a local install of VEP 84. We are leveraging the —flag_pick_allele and —pick_order options. </div>
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<div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px">This is an example of how we are running VEP:</div>
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<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo">perl <a href="http://variant_effect_predictor.pl" target="_blank">
variant_effect_predictor.pl</a> --offline --flag_pick_allele <span style="background-color:rgb(255,255,0)">
-pick_order canonical,rank</span> --merged --dir_cache variant_effect_predictor/cache-dir -i CDH23.1kg.phase3.v5a.EUR.NO-GT.SPLIT-LFT_ALGN.vcf.gz --plugin CADD,whole_genome_SNVs.tsv.gz,InDels.tsv.gz --vcf -o CDH23.1kg.phase3.v5a.EUR.NO-GT.SPLIT-LFT_ALGN.VEP-CADD.vcf
--stats_file CDH23.1kg.phase3.v5a.EUR.NO-GT.SPLIT-LFT_ALGN.VEP-CADD.html —force_overwrite</p>
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<div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px">I noticed that in annotating some of the variants, it does not seem to select the transcript using my pick order as I would expect. I am assuming that the canonical transcript is
defined by: <a href="http://www.ensembl.org/Help/Glossary?id=346" target="_blank">http://www.ensembl.org/Help/Glossary?id=346</a></div>
<div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px"> </div>
<div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px">Example Variants:</div>
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10<span style="white-space:pre-wrap"> </span>73558128<span style="white-space:pre-wrap"></span>rs41281334<span style="white-space:pre-wrap">
</span>G<span style="white-space:pre-wrap"></span>A<span style="white-space:pre-wrap">
</span>.<span style="white-space:pre-wrap"></span>PASS<span style="white-space:pre-wrap">
</span>AC=34;AN=1006</p>
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10<span style="white-space:pre-wrap"> </span>73558886<span style="white-space:pre-wrap"></span>rs4747194<span style="white-space:pre-wrap">
</span>G<span style="white-space:pre-wrap"></span>A<span style="white-space:pre-wrap">
</span>.<span style="white-space:pre-wrap"></span>PASS<span style="white-space:pre-wrap">
</span>AC=280;AN=1006</p>
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The annotation provided for 10:73558128 (rs41281334) is as follows. The picked transcript is <span style="background-color:rgb(255,255,0)">NM_022124.5</span> (which is what I expected since it is the canonical transcript according to the UCSC table query,
and had high rank)</p>
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<span style="background-color:rgb(255,255,0)">A|missense_variant|MODERATE|CDH23|64072|Transcript|NM_022124.5|protein_coding|50/70||||7237|6847|2283|V/I|Gtc/Atc|||1||1||||4.949|0.225802</span></p>
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A|missense_variant|MODERATE|CDH23|64072|Transcript|NM_001171934.1|protein_coding|3/22||||444|127|43|V/I|Gtc/Atc|||1||||||4.949|0.225802</p>
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A|missense_variant|MODERATE|CDH23|64072|Transcript|NM_001171933.1|protein_coding|3/23||||444|127|43|V/I|Gtc/Atc|||1||||||4.949|0.225802</p>
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A|missense_variant|MODERATE|CDH23|ENSG00000107736|Transcript|ENST00000224721|protein_coding|49/69||||6867|6862|2288|V/I|Gtc/Atc|||1|||HGNC|13733||4.949|0.225802</p>
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A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CDH23|ENSG00000107736|Transcript|ENST00000475158|processed_transcript|2/21||||383|||||||1|||HGNC|13733||4.949|0.225802</p>
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A|missense_variant|MODERATE|CDH23|ENSG00000107736|Transcript|ENST00000398788|protein_coding|3/23||||444|127|43|V/I|Gtc/Atc|||1|||HGNC|13733||4.949|0.225802</p>
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<div><font face="Calibri,sans-serif" style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px">The annotation provided for 10: </font><span style="color:rgb(0,0,0);font-family:Menlo;font-size:11px">73558886 (r</span><font face="Menlo" size="2">s4747194)</font><span style="color:rgb(0,0,0);font-family:Menlo;font-size:11px"> is
as follows. The picked transcript is </span><span style="color:rgb(0,0,0);font-family:Menlo;font-size:11px;background-color:rgb(255,255,0)">ENST00000398788.</span><font face="Menlo" size="2" style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px">
<b>QUESTION: Why was it not canonical transcript </b></font><span style="color:rgb(0,0,0);font-family:Menlo;font-size:11px"><b><span style="background-color:rgb(0,255,255)">NM_022124.5</span> which has the same rank?</b></span></div>
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<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo">A|missense_variant|MODERATE|CDH23|64072|Transcript|NM_001171934.1|protein_coding|4/22||||670|353|118|R/Q|cGg/cAg|||1||||||21.7|2.866040</p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo">A|missense_variant|MODERATE|CDH23|64072|Transcript|NM_001171933.1|protein_coding|4/23||||670|353|118|R/Q|cGg/cAg|||1||||||21.7|2.866040</p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo">A|missense_variant|MODERATE|CDH23|ENSG00000107736|Transcript|ENST00000224721|protein_coding|50/69||||7093|7088|2363|R/Q|cGg/cAg|||1|||HGNC|13733||21.7|2.866040</p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><span style="background-color:rgb(255,255,0)">A|missense_variant|MODERATE|CDH23|ENSG00000107736|Transcript|ENST00000398788|protein_coding|4/23||||670|353|118|R/Q|cGg/cAg|||1||1|HGNC|13733||21.7|2.866040</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo">A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CDH23|ENSG00000107736|Transcript|ENST00000475158|processed_transcript|3/21||||609|||||||1|||HGNC|13733||21.7|2.866040</p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><span style="background-color:rgb(0,255,255)">A|missense_variant|MODERATE|CDH23|64072|Transcript|NM_022124.5|protein_coding|51/70||||7463|7073|2358|R/Q|cGg/cAg|||1||||||21.7|2.866040</span></p>
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Thanks so much for your help. Please let me know if I need to post to an alternate forum.</p>
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Ann</p>
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<div><font><font face="Calibri" color="#7f007f">Ann Black-Ziegelbein</font></font></div>
<div><font face="Calibri" color="#7f007f">Senior Application Developer</font></div>
<div><span style="font-family:Calibri"><font color="#7f007f">Molecular Otolaryngology and Renal Research Laboratories </font></span></div>
<div><span style="font-family:Calibri"><font color="#7f007f">University of Iowa</font></span></div>
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