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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>My apologies Will, but I think you are missing a bit of my problem.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>This not a non-variant variation for the remaining individuals/samples . Why are they not being output?<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Cheers<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><br>Duarte<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org] <b>On Behalf Of </b>Will McLaren<br><b>Sent:</b> 27 August 2013 14:45<br><b>To:</b> Ensembl developers list<br><b>Subject:</b> Re: [ensembl-dev] bug in the VEP annotation of VCFs with multiple individuals<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Hi Duarte,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Thanks for raising this. There's an interesting quirk here which seems to be what you're looking at. However, I _do_ see lines of output for the other 8 individuals in the file.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>What is it you would expect to see for sample9? Would you expect that line to be excluded from the output?<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>The reason it is shown is because you are using most_severe, which forces the VEP to give the most severe consequence per variant (which I would generally advise against using!) - when using --individual each individual/variant combination is considered as an independent variant.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>The reason it is intergenic_variant is because that is the "default" consequence - since the locus is non-variant for sample9, it does not go through the consequence prediction, but because you are forcing it to be printed out with most_severe, the VEP has to default to using intergenic_variant.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>I could see two solutions - either excluding the line (since it is non-variant), or having some sort of "no consequence" type - which I am loathe to do as this doesn't fit in to our SO schema.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Will<o:p></o:p></p></div></div><div><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p><div><p class=MsoNormal>On 27 August 2013 12:16, Duarte Molha <<a href="mailto:duartemolha@gmail.com" target="_blank">duartemolha@gmail.com</a>> wrote:<o:p></o:p></p><div><p class=MsoNormal>Dear Developers<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>I believe there is another bug in the VEP when dealing with input VCFs with multiple individuals...<o:p></o:p></p></div><div><p class=MsoNormal>Please take a look at this VCF input and the corresponding output:<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>INPUT VCF line:<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p>#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9<o:p></o:p></p><p>1 876499 . A G 2900.87 PASS AC=15;AF=0.938;AN=16;BaseQRankSum=1.636;DP=92;Dels=0.00;FS=0.000;HRun=6;HaplotypeScore=0.4159;MQ=59.36;MQ0=0;MQRankSum=1.274;QD=31.53;ReadPosRankSum=-0.482;SB=-1653.87;set=variant2 GT:AD:DP:GQ:PL 1/1:0,9:9:24.07:303,24,0 1/1:0,10:10:27.09:365,27,0 0/1:5,4:9:99:104,0,166 1/1:0,7:7:18.04:220,18,0 1/1:0,16:16:39.13:534,39,0 1/1:0,12:12:30.10:407,30,0 1/1:0,14:14:39.13:535,39,0 1/1:0,15:15:36.12:483,36,0 ./.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>OUTPUT annotation file:<o:p></o:p></p></div><div><p>#Uploaded_variation Location Existing_variation Allele ZYG Gene Feature Feature_type Consequence GMAF IND<o:p></o:p></p><p>1_876499_A 1:876499 rs4372192 - HOM - - - intergenic_variant A:0.0824 sample9<o:p></o:p></p></div><div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>As you can see, the annotation output only contains 1 line and it is for the individual that has no genotype call (./.)<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Also, the variation name does not contain the ref/alt_allele information on the name as all other variations. I would expect if to be called 1_876499_A/G<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>For reference here are the config options I used:<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p>host [internalserver]user [user]<o:p></o:p></p><p>password [password]<o:p></o:p></p><p>db_version 72 <o:p></o:p></p><p>port 3306 <o:p></o:p></p><p>species homo_sapiens<o:p></o:p></p><p> <o:p></o:p></p><p>####### runtime options #############<o:p></o:p></p><p>buffer_size 40000<o:p></o:p></p><p>most_severe 1<o:p></o:p></p><p>check_existing 1<o:p></o:p></p><p>check_alleles 1<o:p></o:p></p><p>individual all<o:p></o:p></p><p>fork 6<o:p></o:p></p><p> verbose 1<o:p></o:p></p><p> gmaf 1<o:p></o:p></p><p>filter_common 1<o:p></o:p></p><p>fields Uploaded_variation,Location,Existing_variation,Allele,ZYG,Gene,Feature,Feature_type,Consequence,GMAF,IND<o:p></o:p></p><p><o:p> </o:p></p><p>####### cache stuff ############# <o:p></o:p></p><p>cache 1<o:p></o:p></p><p>dir_plugins /NGS_Test/vep_72_testing/Plugins/<o:p></o:p></p><p>dir_cache /ReferenceData/vep_cache<o:p></o:p></p><p># cache_region_size 1MB<o:p></o:p></p><p>#offline 1<o:p></o:p></p><p># skip_db_check 1<o:p></o:p></p><p><o:p> </o:p></p></div></div></div><p class=MsoNormal style='margin-bottom:12.0pt'><br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>