obtaining summary stat back from locus zoom for rsids?

[Kamyar Sharifi]

Maybe wishful thinking, but I’m wondering if anyone has experience getting rsids back from LocusZoom for a full GWAS summary-statistics file.

There is an option that allows to download summary stat back but it only contains subsets of the variants rather than the complete genome-wide file. I wonder if this is connection issue and we can download the full stat back?  

Also, curious to ask if anyone found a way to download the full LocusZoom-annotated summary statistics with the rsids included, or another straightforward way to recover rsids for the entire GRCh37 file?

Best,

Kam

[locuszoom]

If you're referring to my.locuszoom.org: there should be a "Download summary statistics" button at the top of a GWAS page, like this one: https://my.locuszoom.org/gwas/892646/. It should allow downloading the full set of summary statistics. Some of the rsIDs will not be available of course since not all variants have an rsID available. 

Otherwise there are tools out there that can annotate rsIDs for your file, like annovar or even bcftools + the dbSNP VCF. 

[Kamyar Sharifi]

Thank you for this response -- the download comes back truncated and won't give me the full summary stat...

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