Question: ENSEMBL VEP Inconsistent Results
gravatar for azmanr
2.9 years ago by
azmanr0 wrote:

For my chromosome 12 vcf zebrafish file I ran the online VEP tool last Friday and got some splice donor variants. I generated sequence around those mutations and ran BLAT to confirm their location as I was not getting location for most of my variants on the online list. When I downloaded the vcf file, I was able to find the location of each SNP shown below:

12  26435439    .   T   C   182.0   .   DP=10;VDB=0.134851;SGB=-0.651104;MQSB=0.750668;MQ0F=0;AC=2;AN=2;DP4=0,0,3,5;MQ=57;ANN=C|intron_variant|MODIFIER|RP11-283G6.4|ENSG00000256234|transcript|ENST00000540392|antisense|2/3|n.130+43878A>G||||||,C|intron_variant|MODIFIER|SSPN|ENSG00000123096|transcript|ENST00000534829|processed_transcript|2/3|n.155-15759T>C||||||,C|intron_variant|MODIFIER|SSPN|ENSG00000123096|transcript|ENST00000544231|processed_transcript|3/3|n.317-4977T>C||||||,C|intron_variant|MODIFIER|RP11-283G6.5|ENSG00000255750|transcript|ENST00000540625|antisense|1/2|n.119+37096A>G||||||;CSQ=C|downstream_gene_variant|MODIFIER|chad|ENSDARG00000045071|Transcript|ENSDART00000066264|protein_coding||||||||||rs500634266|1100|1||ZFIN_ID|||P1||||,C|splice_region_variant&intron_variant|LOW|acsf2|ENSDARG00000061201|Transcript|ENSDART00000087040|protein_coding||9/16||||||||rs500634266||-1||ZFIN_ID|||P1||||,C|downstream_gene_variant|MODIFIER|acsf2|ENSDARG00000061201|Transcript|ENSDART00000132737|protein_coding||||||||||rs500634266|3391|-1|cds_end_NF|ZFIN_ID|||||||,C|downstream_gene_variant|MODIFIER|acsf2|ENSDARG00000061201|Transcript|ENSDART00000143213|protein_coding||||||||||rs500634266|3633|-1|cds_end_NF|ZFIN_ID|||||||,C|splice_region_variant&intron_variant|LOW|acsf2|ENSDARG00000061201|Transcript|ENSDART00000163931|protein_coding||8/15||||||||rs500634266||-1||ZFIN_ID|||P1||||    GT:PL   1/1:209,21,0

On Monday, I saw the same results as before, but yesterday, when I opened up the same job, all of a sudden all the splice variants were missing and every variant had a location. I initially thought it must be because of filtering, but I followed the link below that I sent on Friday and still get different results.

I tried to download VEP offline, but my new Mac machine seems to be missing many of the components to run the VEP perl script, and reinstalling all those small software packages in the right format for VEP is not trivial. So I now have rerun the same vcf job again and seem to get the results from yesterday, but I have downloaded an annotated vcf file from Friday with variants not present online, for the same file.

Here is the link to the job:;tl=PGWlyZJssfjMBfZA-4038058

Thanks, Azman

vep ensembl • 892 views
ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by azmanr0

I'm reporting this to the developers in Ensembl.

ADD REPLYlink written 2.9 years ago by Emily_Ensembl21k

We've just been looking at your input file. It looks like you've previously annotated this VCF using SnpEff GRCh37 human annotation. Is this a VCF from human or zebrafish? Why have you switched species on your annotation?

ADD REPLYlink written 2.9 years ago by Emily_Ensembl21k

Hi Emily,

Thanks for your response. My apologies I made that mistake previously and may have posted the wrong file. That being said, the incorrect file and the correct file are similar containing splice donor variants. Even with the incorrect file, I was using the same file for all my previous jobs from Friday, but got inconsistent results. I have ran the correct file with snpEff and confirm that I have splice variants along with running BLAT on the nearby sequencing. I don't get why I am getting inconsistencies, I have shared the correct file with the helpdesk.

Thanks, Azman

ADD REPLYlink written 2.9 years ago by azmanr0
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