<div dir="ltr"><p class="">Hi Devs</p>

<p class=""> I have been trying to run a VCF file by the variant
annotation script and I've been getting a warning message that I have never
before encountered..</p><p class=""></p>

<p class=""> I was wondering if someone could let me know if it is
something I am doing wrong…</p><p class=""></p>

<p class=""> The message is :</p><p class=""></p>

<p class=""> <b>Can't call method "expand" on an undefined value
at <sic>/Bio/EnsEMBL/Variation/VariationFeature.pm line 471</b></p><p class=""><b></b></p>

<p class=""><b> </b></p>

<p class="">Here are the configuration options I am using:</p>

<p class=""> </p>

<p class="">Configuration options:</p>

<p class=""> ###</p><p class=""></p>

<p class="">allow_non_variant    1</p>

<p class="">cache                1</p>

<p class="">canonical            1</p>

<p class="">ccds                 1</p>

<p class="">check_alleles        1</p>

<p class="">check_existing       1</p>

<p class="">config              
vep_human.ini</p>

<p class="">core_type           
core</p>

<p class="">custom              
./vep_additional_annotations/Somatic_variation_phenotypes.bed.gz,Somatic,bed,exact
./vep_additional_annotations/dbsnp135_ensembl_variation_phenotype.bed.gz,dbsnp135,bed,exact</p>

<p class="">db_version          
72</p>

<p class="">dir                 
/ReferenceData/vep_cache</p>

<p class="">dir_cache           
/ReferenceData/vep_cache</p>

<p class="">dir_plugins         
./Plugins</p>

<p class="">domains              1</p>

<p class="">force_overwrite      1</p>

<p class="">fork                 5</p>

<p class="">gmaf                 1</p>

<p class="">hgnc                 1</p>

<p class="">host                
<a href="http://ensembldb.ensembl.org">ensembldb.ensembl.org</a></p>

<p class="">individual           all</p>

<p class="">input_file           All_BOTH_SNPINDELfilter_PASSED.vcf</p>

<p class="">maf_1kg              1</p>

<p class="">numbers              1</p>

<p class="">output_file          All_BOTH_SNPINDELfilter_PASSED.ann</p>

<p class="">plugin              
OGT_NHBLI_MAF,/ReferenceData/NHLBI_EVS/NHLBI_OGT.gz        OGT_selected_VCF_fields_output  Blosum62        Carol  
OGT_Condel,b    OGT_Grantham    TSSDistance     Downstream</p>

<p class="">polyphen             b</p>

<p class="">port                
5306</p>

<p class="">protein              1</p>

<p class="">regulatory           1</p>

<p class="">sift                 b</p>

<p class="">species             
homo_sapiens</p>

<p class="">stats               
HASH(0x4370ad8)</p>

<p class="">terms               
SO</p>

<p class="">verbose              1</p>

<p class=""> </p>

<p class="">I would be very grateful for your help.</p>

<p class=""> Duarte Molha</p>
</div>