LD not loading in the plot

[alan mejia]

Hi,

I have been uploading files in the required format. I have already 4 files and the LD info is automatically loaded in the plot. Never had an issue.

However, when I try to load a 5th file, in the same exact format, the LD is not loaded in the plot. I thought there was a limit but it doesn't seem to be the case. I re-uploaded some files and the LD info is not shown. 

When I try to submit the rs recognizes only chr:position not chr:position_REF/ALT. Then, the LD is not loaded in the plot.

Any thought?

Thanks

[alan mejia]

I went back to my original VCF, kept allele order, and run GWAS again. It didn't work!

It seems that LD data from GRCh37 are not being loaded in the focus region. rs is loaded as chr:pos when submitting the file, even if in the file is as --> chr:pos_REF/ALT

Any thought?

Thanks

[Matthew Maher]

In my experience, this invariably means that the alleles are not properly aligned to REF/ALT .  i.e. it's not a problem with the file format, but rather the file contents.   To avoid confusion about the construction of that Marker Name (i.e. are you sure they are really CHR:POS_REF/ALT ? or are they CHR:POS_ALT/REF ? or maybe CHR:POS_MAJOR/MINOR... or something else etc) you should use the 'variant from column' input option so you can specifically identify the "REF" and "ALT" columns in your input.  If you don't have "REF" and "ALT" columns in the input, then you would need to figure out how to make them.  Many summary stats files only care about effect/tested-allele versus other-allele and have markers constructed completely independent of the reference.

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