Error in uploading data, even after sorting per chromosome and position

[Alia Saeed]

Hi,

I have been using locusZoom for quite some time now, and it usually works faultlessly however, I have been trying for two days now to upload this GWAS data and it gives me the same error message no matter what reformatting and edits I do to my file (attached GWAS_file).

The error is very vague:  "Validation error. Check that all column options are specified correctly. Your file must be sorted by chromosome and position prior to upload"

Note that I manually pick what each column represents, I tick that it is -log10(p) and have ordered everything as needed.

Has anyone encountered this before? I think my file is formatted correctly, but can I please ask for a second pair of eyes to take a look maybe?

Many thanks,

Alia

[Andy Boughton]

Thanks for your inquiry!

When I open the sorted file, I notice three lines like this:

1       100015528       

1       1000156 

1       100015703

This is because by default, the sort utility reads text like a human. It needs to be told to read numbers like a computer instead. If you had a VCF-like file (col 1 = chrom, col 2 = pos), we often suggest a sort command like the following:

sort -k1,1V -k2,2n

This tells it to compare the positions as numbers, which would give a more correct order. Hope this helps!

-Andy Boughton
abo...@umich.edu

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

--
You received this message because you are subscribed to the Google Groups "locuszoom" group.
To unsubscribe from this group and stop receiving emails from it, send an email to locuszoom+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/locuszoom/fd9960cb-cbc7-4bf0-8a07-ffaaef7b60d8n%40googlegroups.com.

[Alia Saeed]

This works now. Thank you so much! 

Can I please ask why SNPs in LD sometimes just don't show? In the file used here (attached above), I have provided the chr:pos:ref_allele:alt_allele and the rsid, as needed, but everything is marked in grey.

[Andy Boughton]

The most common reasons:

https://my.locuszoom.org/about/#missing-ld

-Andy Boughton
abo...@umich.edu

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

To view this discussion on the web visit https://groups.google.com/d/msgid/locuszoom/58050ce8-385c-49f0-83a6-20c9e867f87an%40googlegroups.com.