[ensembl-dev] bug in the VEP annotation of VCFs with multiple individuals

[Duarte Molha]

Dear Developers

I believe there is another bug in the VEP when dealing with input VCFs with
multiple individuals...
Please take a look at this VCF input and the corresponding output:

INPUT VCF line:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9

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      ./.


OUTPUT annotation file:

#Uploaded_variation     Location        Existing_variation      Allele
ZYG     Gene    Feature Feature_type    Consequence     GMAF    IND

1_876499_A      1:876499        rs4372192       -       HOM     -
-       -       intergenic_variant      A:0.0824         sample9

As you can see, the annotation output only contains 1 line and it is for
the individual that has no genotype call (./.)

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

For reference here are the config options I used:

host
[internalserver]user
[user]

password                                            [password]

db_version        72

port                                                       3306

species                                                 homo_sapiens



#######     runtime options  #############

buffer_size                                         40000

most_severe                     1

check_existing                  1

check_alleles                     1

individual                                             all

fork                                                        6

 verbose                                                               1

 gmaf                                                      1

filter_common                  1

fields
Uploaded_variation,Location,Existing_variation,Allele,ZYG,Gene,Feature,Feature_type,Consequence,GMAF,IND


#######     cache stuff   #############

cache                                                    1

dir_plugins
/NGS_Test/vep_72_testing/Plugins/

dir_cache
/ReferenceData/vep_cache

# cache_region_size       1MB

#offline                                                1

# skip_db_check                              1
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