LocalZoom, LocusZoom.js, and tabix indexed file

[jie huang]

Dear Andy:

I now read your BioRxiv paper. Congratulations! About 10 years ago, I communicated with Ryan (Welch) on Locuszoom. It is good to see that he is still a contributing author for your new paper.

The supplementary table S1 compares features of "LocusZoom.js" and "LoculZoom" and "my.locuszoom.org". This is the first time I noticed there is a Loc*al*Zoom. But wait, this URL https://statgen.github.io/localzoom/ says "LocalZoom: Plot your own data with LocusZoom.js". So, does LocalZoom actually meansLocusZoom.js? Now I am a bit confused here. Will these 3 eventually have all the same features implemented?

"Stack multiple GWAS in one view" is a very nice feature that I want to use. It is a pity that my.locuszoom.org currently does not have that feature. Will I see multiple GWAS manhattan plots or just locuszoom plots for a particular region? I guess it is NOT the manhattan plot, because table S1 shows that Locuszoom.js and LocalZoom does not even have the feature of "Manhattan Plot".

The URL https://statgen.github.io/localzoom/ requires me to upload a tabix indexed file. Previously I have used tabix to index a VCF file and a standard BED file. How could I use tabix to index a standard GWAS output file (such that from PLINK)? Right now, I got error messages of "[E::get_intv] failed to parse TBX_GENERIC, was wrong -p [type] used?" for every line in my input GWAS file.

Thank you & best regards,

Jie

[Andrew Boughton]

Yes, I'm very grateful that Ryan has been a part of the team for both papers- his expertise has been a tremendous asset! To answer your question about the differences between tools:

LocusZoom.JS is the basic rendering library. It can be highly customized, but you need to write your own code to use it with your own data.

LocalZoom (and my.locuszoom.org) are the "glue code" required to make plots with your own data. They handle opening files and parsing into a form the web browser can read. Some websites, like the t2dkp, have their own way of fetching data; they use locuszoom.js as a separate piece.

LocalZoom operates on local files, and is especially aimed at people who don't want to trust uploads to third party server. It does not summarize the file because it does not read it all at once into memory; this would be slow and might crash the web browser. 

Eventually I'd like to add "plot multiple tracks" to my.locuszoom.org, but since it would ideally use a mix of personal and third party datasets, we will want to improve the search and metadata features first, so that we don't suggest tracks that are not of interest. (Some of the public datasets shared by users at present have titles like "aaaa", which would be a bad user experience)

For your tabix question: PLINK is an interesting program, in that widely used versions like 1.9 often create space delimited files; tabix requires a tab delimited format. My.locuszoom.org handles file conversion for you and someday we will add space delimited file support; for localzoom this is harder because it does not convert the file, and the limitation is in a separate tool (tabix).

-Andy Boughton

abo...@umich.edu

On Jan 4, 2021, at 7:00 PM, jie huang <jiehu...@gmail.com> wrote:



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[jie huang]

Dear Andy:

Thank you again for your clarification!

I did use TAB in my input GWAS file, but I still get error messages of "[E::get_intv] failed to parse TBX_GENERIC, was wrong -p [type] used?" for every line in my input GWAS file, when I run "tabix my.GWAS.gz", after I run "bgzip my.GWAS". Do you know how to use tabix to index a GWAS file with a lot of columns such as "CHR POS SNP REF ALT A1 A2 FREQ BETA SE P Z N"?

Best regards,

Jie