<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>