<div dir="ltr">Hi Duarte,<div><br></div><div>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.</div>
<div><br></div><div>What is it you would expect to see for sample9? Would you expect that line to be excluded from the output?</div><div><br></div><div>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.</div>
<div><br></div><div>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.</div>
<div><br></div><div>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.</div>
<div><br></div><div>Will</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 27 August 2013 12:16, 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">Dear Developers<div><br></div><div>I believe there is another bug in the VEP when dealing with input VCFs with multiple individuals...</div>
<div>Please take a look at this VCF input and the corresponding output:</div>
<div><br></div><div>INPUT VCF line:</div><div><br></div><div><p>#CHROM POS
ID REF
ALT QUAL FILTER
INFO FORMAT
sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9</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 ./.</p><p></p>
</div><div><br></div><div>OUTPUT annotation file:</div><div><p>#Uploaded_variation
Location
Existing_variation Allele
ZYG Gene Feature
Feature_type Consequence
GMAF IND</p>
<p>1_876499_A
1:876499
rs4372192
- HOM
- -
-
intergenic_variant
A:0.0824 sample9</p></div><div><div><br></div><div>As you can see, the annotation output only contains 1 line and it is for the individual that has no genotype call (./.)</div><div><br></div><div>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</div>
<div><br></div><div>For reference here are the config options I used:</div><div><br></div><div><p>host [internalserver]user [user]</p>
<p></p>
<p>password [password]</p>
<p>db_version
72 </p>
<p>port
3306 </p>
<p>species
homo_sapiens</p>
<p> </p>
<p>####### runtime options
#############</p>
<p>buffer_size
40000</p>
<p>most_severe
1</p>
<p>check_existing
1<br></p><p></p>
<p>check_alleles
1<br></p><p></p>
<p>individual
all<br></p><p></p>
<p>fork
6<br></p><p></p>
<p> verbose
1</p>
<p> gmaf
1</p>
<p>filter_common
1<br></p><p></p>
<p>fields
Uploaded_variation,Location,Existing_variation,Allele,ZYG,Gene,Feature,Feature_type,Consequence,GMAF,IND<br></p>
<p><br></p>
<p>####### cache stuff
############# </p>
<p>cache
1</p>
<p>dir_plugins
/NGS_Test/vep_72_testing/Plugins/</p>
<p>dir_cache
/ReferenceData/vep_cache</p>
<p># cache_region_size 1MB</p>
<p>#offline
1</p>
<p>#
skip_db_check
1</p>
<p><br></p></div><div>
</div></div></div>
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<br></blockquote></div><br></div>