[ensembl-dev] Bug with HGVS Representation while running VEP

[Sarah Hunt]

Hi Priti,

We have seen this issue when there are problems with the fasta file or 
it's index. If you are happy the fasta file is fine, deleting the index 
file and letting VEP re-build it usually resolves the poblem. Also, do 
check you are using BioPerl version 1.6.1 or later as we have seen 
problems with earlier versions.

Best wishes,

Sarah

On 21/01/2016 16:15, Priti Kumari wrote:
>
> Hello,
>
> I ran two instances of VEPv83 on a large file with 50000 variants. I 
> am getting different output, when I compare two output files. One, 
> example is different c. value.
> v1 :
> PTEN  0       .       GRCh37  10      89692904 89692904        +       
> Nonsense_Mutation       SNP     C C       T       
> rs121909224             TUMOR   NORMAL  C C c.388G>T p.Arg130Ter     
> p.R130* ENST00000371953
>
> v2:
> PTEN  0       .       GRCh37  10      89692904 89692904        +       
> Nonsense_Mutation       SNP     C C       T       
> rs121909224             TUMOR   NORMAL  C C c.388C>T p.Arg130Ter     
> p.R130* ENST00000371953
>
> Command used for running both instances :
>
> /usr/bin/perl variant_effect_predictor//variant_effect_predictor.pl 
> --species homo_sapiens --assembly GRCh37 --offline --no_progress 
> --no_stats --sift b --ccds --uniprot --hgvs --symbol --numbers 
> --domains --gene_phenotype --regulatory --canonical --protein 
> --biotype --uniprot --tsl --pubmed --variant_class --shift_hgvs 1 
> --check_existing --check_alleles --check_ref --total_length 
> --allele_number --no_escape --xref_refseq --failed 1 --vcf --minimal 
> --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length 
> --dir .vep/ --fasta 
> .vep/homo_sapiens/83_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa 
> --input_file OP_VARIANT.vcf --output_file OP_VARIANT.v1.vep.vcf 
> --polyphen b --gmaf --maf_1kg --maf_esp --plugin 
> ExAC,/.vep//ExAC.r0.3.sites.minus_somatic.vcf.gz --fork 4
>
> Any idea why this is happening?
> Thank you,
> -- 
> Priti Kumari
> Bioinformatics Engineer
> Department of Biostatistics and Computational Biology
> Dana-Farber Cancer Institute
> 3 Blackfan Cir,
> Center for Life Science Boston, Room 11037,
> Boston, MA 02115
> 617-632-6133
>
>
>
>
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