<div dir="ltr">Ah, sorry, I wasn't testing with --filter_common.<div><br></div><div>However, if I add --filter_common, I don't see any lines in the output, and the VEP reports all 9 variants/individuals are being filtered out. rs4372192 overlaps and has a frequency of 0.08.</div>
<div><br></div><div>Perhaps your API and/or script is out of date? Though I still don't see the problem even if I test it with v71...</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On 27 August 2013 15:03, Duarte Molha <span dir="ltr"><<a href="mailto:duartemolha@gmail.com" target="_blank">duartemolha@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">My script does not output any information for the remaining 8 samples. If I understand correctly from your email, your script is outputting the other samples.<div><br></div><div>What might be causing the discrepancy?</div>
<div><br></div><div>Best regards</div><div><br></div><div>Duarte</div><div><br></div></div><div class="gmail_extra"><br clear="all"><div><font style color="#999999">=========================<br>
Duarte Miguel Paulo Molha <br></font><div><font style color="#999999"> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a> <br>=========================</font></div>
</div><div><div class="h5">
<br><br><div class="gmail_quote">On Tue, Aug 27, 2013 at 2:50 PM, Duarte Molha <span dir="ltr"><<a href="mailto:Duarte.Molha@ogt.com" target="_blank">Duarte.Molha@ogt.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-GB" link="blue" vlink="purple"><div><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.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></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?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Cheers<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><br>Duarte<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></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""> <a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a> [mailto:<a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a>] <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<u></u><u></u></span></p><div><div><p class="MsoNormal">
<u></u> <u></u></p><div><p class="MsoNormal">Hi Duarte,<u></u><u></u></p><div><p class="MsoNormal"><u></u> <u></u></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.<u></u><u></u></p>
</div><div><p class="MsoNormal"><u></u> <u></u></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?<u></u><u></u></p></div><div><p class="MsoNormal">
<u></u> <u></u></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.<u></u><u></u></p>
</div><div><p class="MsoNormal"><u></u> <u></u></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.<u></u><u></u></p>
</div><div><p class="MsoNormal"><u></u> <u></u></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.<u></u><u></u></p>
</div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Will<u></u><u></u></p></div></div><div><p class="MsoNormal" style="margin-bottom:12.0pt"><u></u> <u></u></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:<u></u><u></u></p>
<div><p class="MsoNormal">Dear Developers<u></u><u></u></p><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">I believe there is another bug in the VEP when dealing with input VCFs with multiple individuals...<u></u><u></u></p>
</div><div><p class="MsoNormal">Please take a look at this VCF input and the corresponding output:<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">INPUT VCF line:<u></u><u></u></p>
</div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p>#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9<u></u><u></u></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 ./.<u></u><u></u></p>
</div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">OUTPUT annotation file:<u></u><u></u></p></div><div><p>#Uploaded_variation Location Existing_variation Allele ZYG Gene Feature Feature_type Consequence GMAF IND<u></u><u></u></p>
<p>1_876499_A 1:876499 rs4372192 - HOM - - - intergenic_variant A:0.0824 sample9<u></u><u></u></p></div><div><div><p class="MsoNormal"><u></u> <u></u></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 (./.)<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></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<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p>
</div><div><p class="MsoNormal">For reference here are the config options I used:<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p>host [internalserver]user [user]<u></u><u></u></p>
<p>password [password]<u></u><u></u></p><p>db_version 72 <u></u><u></u></p><p>port 3306 <u></u><u></u></p>
<p>species homo_sapiens<u></u><u></u></p><p> <u></u><u></u></p><p>####### runtime options #############<u></u><u></u></p><p>buffer_size 40000<u></u><u></u></p>
<p>most_severe 1<u></u><u></u></p><p>check_existing 1<u></u><u></u></p><p>check_alleles 1<u></u><u></u></p><p>individual all<u></u><u></u></p>
<p>fork 6<u></u><u></u></p><p> verbose 1<u></u><u></u></p><p> gmaf 1<u></u><u></u></p>
<p>filter_common 1<u></u><u></u></p><p>fields Uploaded_variation,Location,Existing_variation,Allele,ZYG,Gene,Feature,Feature_type,Consequence,GMAF,IND<u></u><u></u></p><p><u></u> <u></u></p><p>####### cache stuff ############# <u></u><u></u></p>
<p>cache 1<u></u><u></u></p><p>dir_plugins /NGS_Test/vep_72_testing/Plugins/<u></u><u></u></p><p>dir_cache /ReferenceData/vep_cache<u></u><u></u></p>
<p># cache_region_size 1MB<u></u><u></u></p><p>#offline 1<u></u><u></u></p><p># skip_db_check 1<u></u><u></u></p><p><u></u> <u></u></p></div>
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