Only SNPs in LD on the right of reference SNP is colored

[hui wang]

Hi,

I used my own LD file. It is prepared according to the instructions on the locuszoom website.

But each time I selected a reference SNP, only the SNPs on the rightside of the plot and are in LD with this SNP are colored. Even though there are SNPs on the leftside of the plot that are in LD with the SNP, but they are not colored. Could please please help with this?  I wonder if this is bug? Thank you!

[Andy Boughton]

At a quick glance, it really looks as though you prepared your LD file in a much narrower range than what the plot shows by default. (check the ld-window and ld-window-kb values)

Eg, we can only show the LD in the region you give us data for.  By default, we show data in a fairly wide range around the specified variant (either a 500kb or 1mb wide window, if I remember correctly). Did you provide LD information over that full range?

-Andy Boughton
abo...@umich.edu

Applications Programmer/Analyst, Lead
Center for Statistical Genetics
University of Michigan

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[hui wang]

Thank you for your quick reply. I used the LD file for the entire chromosome 1.
Here is another example, if I choose a SNP on the left of the most significant signal as the reference: we can see that it is in LD with the most significant signal.
However, on the original plot that use the most significant SNP as the reference, this SNP is not colored as in LD with the most significant  signal (see the plot in the original post).
The problem is that only the SNPs in LD with the reference SNP and located on the rightside of the reference SNP in the plot are colored.

[hui wang]

Wondering if any one have the same problem?

[yuanl...@gmail.com]

https://genome.sph.umich.edu/wiki/LocusZoom_Standalone#Quick_Start_.28Requirements.29