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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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