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Hi Priti,<br>
<br>
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.<br>
<br>
Best wishes,<br>
<br>
Sarah<br>
<br>
<div class="moz-cite-prefix">On 21/01/2016 16:15, Priti Kumari
wrote:<br>
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cite="mid:20160121161716.D056913444B_6A1048CB@hx-mx2.ebi.ac.uk"
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Hello,<br>
<br>
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.<br>
v1 : <br>
PTEN 0 . GRCh37 10 89692904
89692904 + Nonsense_Mutation SNP C
C T rs121909224 TUMOR NORMAL C
C <font color="#ff0000">c.388G>T</font>
p.Arg130Ter p.R130* ENST00000371953<br>
<br>
v2:<br>
PTEN 0 . GRCh37 10 89692904
89692904 + Nonsense_Mutation SNP C
C T rs121909224 TUMOR NORMAL C
C <font color="#ff0000">c.388C>T</font>
p.Arg130Ter p.R130* ENST00000371953<br>
<br>
Command used for running both instances :<br>
<br>
/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<br>
<br>
Any idea why this is happening?<br>
Thank you,<br>
<pre class="moz-signature" cols="72">--
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</pre>
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