Question: VEP: SIFT- PolyPhen error?
gravatar for ginlucks
5.7 years ago by
ginlucks10 wrote:

Hi all

Some days ago I did an analysis using VEP (I have filtered by maf<7%), than, I filtered results with a score greater than 0.35 in SIFT  and lower than 0.45 in Polyphen, and all works well. I obtained about 148 variants.

Today I would do the same analysis with different filtering (with a lower MAF<5%)  but when I would filter results (SIFT <0.35 -PP> the previous analysis) it show me only five variants.... now I'm sure I should obtain more variants because of in the previous  analysis most of 148 variants have a maf below 5%. Furthermore Sift and PP calculated score just for this 5 variants and not for the other 15.000. 

So my question is: is it possible that today, VEP has some bugs or something else?


I also try to filter my variants with maf <80% but I always obtain 5 variants with calculated score

error vep sift polyphen • 2.8k views
ADD COMMENTlink modified 5.5 years ago by Biostar ♦♦ 20 • written 5.7 years ago by ginlucks10

Can you provide the URL for your analysis? This will allow us to debug if there are any bugs or issues.

ADD REPLYlink written 5.7 years ago by EnsemblWill560

does this link work?;field1=SIFT;operator1=lte;tl=AHwmJghn2arQlgqP-712700;value1=0.35#Results


It is not the link where I'm working on, (it is just a "test")  but a similar one ( I used same option filtering)


thanks for help 

ADD REPLYlink written 5.7 years ago by ginlucks10

I think perhaps you haven't clicked on the "show All" link in the navigation bar.

If I do the first search (MAF < 0.07, SIFT > 0.35, PolyPhen < 0.45), I get 994 results for 973 variants (a few variants map to multiple transcripts/genes):

And if I change the MAF filter to 0.05 I get 858 results from 840 variants:

ADD REPLYlink written 5.7 years ago by EnsemblWill560

You should be able to see the results on this URL (filtered to 5%);field1=GMAF;field2=SIFT;field3=PolyPhen;from=1;operator1=lt;operator2=gte;operator3=lte;tl=AHwmJghn2arQlgqP-712700;to=20490;value1=0.05;value2=0.35;value3=0.45#Results

ADD REPLYlink written 5.7 years ago by EnsemblWill560


On navigation bar I clicked on show all.

However, I saw that you used gmaf filter on the results page. I used this filter to obtain the results. ...maybe the problem is here, (Im sorry Im on tablet at the moment and I cant post pictures as you did)

This is the option I used to set up filtering in output options:

In extra option:

-Identify canonical transcripts

-Protein domains

in filtering options:

-By frequency: -->Advanced filtering --> exclude variant maf greater than 0.05

-Return results for variants in coding regions only

-Restrict results: --> show one selected consequence per gene



EDIT: I re-run analysis without any options, than on results l filtered them by show me again 5 variants only.
ADD REPLYlink modified 5.7 years ago • written 5.7 years ago by ginlucks10

I'm not sure how I can make this any clearer.

By default the preview shows you results for the first 5 variants that pass your filters.

You can page through them with the small arrow icons, or you can show more than 5 by clicking on the numbered links next to the word "Show".

I have done as you have, uploaded your input file with no options changed.

On the results page I see: "Showing 23 results for variants 1-5 of 78547"

If I then add the filter "GMAF < 0.05", I see: "Showing 41 results for variants 1-5". There is no "of N" here since after filtering the VEP does not know how many variants there will be in total (otherwise it would have to scan through the entire results file before showing you this).

I can then, for example, click the "10" link to show results for the first 10 variants, and then click the right arrow to navigate to the next 10.

For more information, hover over the "i" icons on the results page, see the documentation, watch the VEP intro video.


ADD REPLYlink modified 5.7 years ago • written 5.7 years ago by EnsemblWill560

Yes I had understand what you mean....but instead i click on all it show me only 5 variants. However I Try to use vep on another pc and it works.. so i think there is a problem on my pc. I'll try to reinstall browser or upgrade software.

Thanks for help.

ADD REPLYlink written 5.7 years ago by ginlucks10
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