Fail to generate the input file

[Yue Hu]

Hello,

I'm trying to create regional plots through the website: https://statgen.github.io/localzoom/ . But I failed to generate the correct format for the input through the instructions. The dataset I have now is a text file containing the summary statistics from a GWAS analysis. Could you please provide me with more instructions on how to transform the text file I have to an input dataset with correct format?

I used to use the older version of the Locuszoom (http://locuszoom.sph.umich.edu/genform.php?type=yourdata), which allows me to directly input text files. However, it doesn't support GRCh38, that's why I am learning to create regional plots through the first website, but failed to generate the desired output.

Thank you very much for your time and support! Any insights or instructions are appreciated. Looking forward to hearing from you!

Best,

Yue

[Andy Boughton]

Greetings,

This is a very broad question- it's a bit hard to suggest a solution without an idea of the error message, file format, etc. (there are many GWAS programs and some produce nicer output than others) The best general instructions we have are at: https://statgen.github.io/localzoom/#instructions 

As a rough rule, "if you can successfully generate and use a tabix index for the file, then you can probably load the file into LocalZoom". This means that: 

1. The file is tab delimited (not csv, spaces, etc)

2. You've selected the right columns for chrom, pos, etc.

It also helps if your GWAS program doesn't output corrupted values, like "pvalue=0" (numerical underflow) or NaN. A good test of your file is to generate the tabix index, than immediately try to use it to query a specific region via the command line. (the most common mistake I see is that people select the wrong column for chromosome; `tabix -l filename.gz` can be helpful for spotting this)

If you had a specific error message or step of the process where you had issues, I could try to help more. If you're at the stage where you're not sure where to start, it might be useful to grab a friend or labmate and ask them to take a look first- there are MANY file formats out there, which makes it hard to offer one easy answer for everyone.

-Andy Boughton
abo...@umich.edu

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

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