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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><pre>Hi Dr. McLaren,<o:p></o:p></pre><pre>Sorry for the additional query, but I would like to add to my last posted question. As I investigate further, it seems that I don’t understand how the --lrg flag works. Is it adding a second separate annotation if there is an LRG overlap?<br>I notice that when I run the commands:<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>perl variant_effect_predictor.pl --fork 4 --no_stats --everything --lrg --cache --format vcf --force_overwrite --check_existing --check_alleles --vcf --no_progress --pubmed --gmaf --maf_1kg –-pick -i input.vcf –o output.VEP.vcf<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Whenever I get a LRG annotation, there is a separate regular annotation. For example:<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>1 92941604 . C T . . CSQ=T|ENSG00000162676|ENST00000370332|Transcript|synonymous_variant|1570|1251|417|T|acG/acA|COSM1344916|||7/7||||||<o:p></o:p></pre><pre>|-1||YES|GFI1|HGNC||||protein_coding|ENSP00000359357|PROSITE_profiles:PS50157&SMART_domains:SM00355&Superfamily_domains:SSF57667|CCDS30773.1|ENST00000370332.1:c.1251G>A|ENST00000370332.1:c.1251G>A(p.%3D)|||||<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Followed 105 lanes later by:<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>1 92941604 . C T . . CSQ=A|LRG_63|LRG_63t1|Transcript|synonymous_variant|1501|1251|417|T|acG/acA||||7/7|||||||1||YES|LRG_63|LRG||||LRG_g<o:p></o:p></pre><pre>ene|LRG_63p1|||LRG_63t1.1:c.1251G>A|LRG_63t1.1:c.1251G>A(p.%3D)|||||<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>This causes the output .vcf to have out of order variants (no longer properly sorted). Not that this is the same consequence but one shown as the + strand (CSQ=T) and one is shown on the – strand (CSQ=A).<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Am I doing something wrong here?<br><br>Any help would be appreciated.<o:p></o:p></pre><pre>Thanks!<br>Andrew<o:p></o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre>>Thank you very much Dr. McLaren.<o:p></o:p></pre><pre>>Just one clarification to the LRG choice. Is the LRG always presented as the first consequence (if it exists)? If this is true, then if the --pick chooses the worst consequence, and there are multiple transcripts with the same >"worst consequence", does VEP --pick the first transcript with that consequence? If that is true, if the LRG contains the "worst consequence" along with other similar transcripts, will --pick successfully choose this consequence >over other equal transcripts?<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>>Any help on this would be appreciated.<o:p></o:p></pre><pre>>Thank you again!<o:p></o:p></pre><pre>>Andrew<o:p></o:p></pre><pre>><o:p> </o:p></pre><pre>><i>I should also say that there's currently no way to prioritise LRG<o:p></o:p></i></pre><pre>><i>consequences other than filtering using filter_vep.pl, though this wouldn't<o:p></o:p></i></pre><pre>><i>be a complete solution.<o:p></o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>><i>Will<o:p></o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>><i>On 1 April 2014 09:51, Will McLaren <wm2 at ebi.ac.uk<<a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>>> wrote:<o:p></o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>><i> Hi Andrew,<o:p></o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>><i> In fact this is already possible; just add the flag --lrg at runtime. Note<o:p></o:p></i></pre><pre>><i> however that using LRGs depends on connecting to our database, so this will<o:p></o:p></i></pre><pre>><i> not work using --offline and will connect to ensembldb.ensembl.org when<o:p></o:p></i></pre><pre>><i> using --cache. Because of this database connection you may find that the<o:p></o:p></i></pre><pre>><i> script runs more slowly as it attempts to remap your input variants to LRG<o:p></o:p></i></pre><pre>><i> coordinates.<o:p></o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>><i> I'm afraid this is missing from the documentation currently, I will get<o:p></o:p></i></pre><pre>><i> that updated.<o:p></o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>><i> Regards<o:p></o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>><i> Will McLaren<o:p></o:p></i></pre><pre>><i> Ensembl Variation<o:p></o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>><i> On 31 March 2014 22:24, Andrew Carson <acarson at invivoscribe.com<<a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>>> wrote:<o:p></o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>>><i> Hi ensembl-dev team,<o:p></o:p></i></pre><pre>>><i><o:p> </o:p></i></pre><pre>>><i> I was just wondering if there are plans to incorporate the LRG (locus<o:p></o:p></i></pre><pre>>><i> reference genomic) records into the VEP annotation pipeline (from here:<o:p></o:p></i></pre><pre>>><i> <a href="http://www.lrg-sequence.org/home">http://www.lrg-sequence.org/home</a>). I only ask because in the HGVS new<o:p></o:p></i></pre><pre>>><i> clinical reporting guidelines they recommend using the LRG sequence (if one<o:p></o:p></i></pre><pre>>><i> is present) to standardize variant reporting.<o:p></o:p></i></pre><pre>>><i><o:p> </o:p></i></pre><pre>>><i><o:p> </o:p></i></pre><pre>>><i><o:p> </o:p></i></pre><pre>>><i> It would also be very useful to have an option where, if a variant<o:p></o:p></i></pre><pre>>><i> overlaps an LRG, you can choose to "pick" that consequence over other<o:p></o:p></i></pre><pre>>><i> consequences.<o:p></o:p></i></pre><pre>>><i><o:p> </o:p></i></pre><pre>>><i><o:p> </o:p></i></pre><pre>>><i><o:p> </o:p></i></pre><pre>>><i> Any thoughts on if this could be added to the development for the next<o:p></o:p></i></pre><pre>>><i> release cycle?<o:p></o:p></i></pre><pre>>><i><o:p> </o:p></i></pre><pre>>><i> Thanks for all of your help!<o:p></o:p></i></pre><pre>>><i><o:p> </o:p></i></pre><pre>>><i><o:p> </o:p></i></pre><pre>>><i><o:p> </o:p></i></pre><pre>>><i> Andrew R. Carson, Ph.D.</i><o:p></o:p></pre><p class=MsoNormal><o:p> </o:p></p></div></body></html>