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:
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: https://dec2017.archive.ensembl.org/Danio_rerio/Tools/VEP/Results?db=core;tl=PGWlyZJssfjMBfZA-4038058