<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>