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

[Priti Kumari]

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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