Strange gaps between chromosome in Manhattan plot

[Eve]

Hello,

I noticed some strange gaps between chromosome and tails at the end of the chromosome in my Manhattan plot from SNP2GENE output (job 154177). I used the same data and run a Manhattan plot using R by myself and there is no gap in my R output. Anyone knows what's causing the gap from SNP2GENE output?? (I am attaching the plots below)

from SNP2GENE:

from R:

Thanks in advance!

Eve

[d.p.wi...@vu.nl]

Hi Eve,

I am guessing something went wrong with the upload or the first step of FUMA where the data is read in. I can only access the files after they have been processed from the input file and the manhattan plot of these varians look like the one generated by FUMA. 

Can you send me your input file by email? I can investigate why variants are being lost. 

If not, can you share the lines of your input file for a few variants on chr 11 between chr11:153717204 and chr11:214543221? There appears to be no variants in between these in the data on the server so it would be useful to see what the input file for those variants looks like.

Cheers,

Doug

[Melkamu Bedimo Beyene]

Dear FUMA team and users,

I am facing the same problem as this.

Any help to resolve this, please? 

kind regards,

Melkamu 

[Tanya Phung]

Hello, 

Could you please provide:

jobID
The manhattan plot as output from FUMA

Did you also try to plot your file using R as the user above? 

Could you please be more specific as to what the problems are? 

Thank you.

[Melkamu Bedimo Beyene]

Hi Tanya,

Yes, I do in R but have the same gaps in the R plot too. 

The job ID is  496978

Kind regards

[Tanya Phung]

Hello, 

Could you please provide the plots as output from FUMA and from your R plot? 

If gaps appear using multiple methods to plot besides FUMA, then we think that it could be an issue with your input data. 

Thank you,
Tanya