Convert .xls data to something IGV can read?

[Katherine Shortt]

I'm very new to IGV, please bear with me!  I want to use the program to make a Manhattan Plot of a set of data currently in a .xls file.  The file contains SNP name, chromosome, location and Chi-squared p-value.  Do you know to which file type I should convert the data, and what free conversion tool might do the trick?  

Many thanks!

[Nick B]

Hi Katherine, 

I'm not sure that IGV can do this so someone else may be able to tell you if it can. To easily make a Manhattan plot I use Galaxy: https://main.g2.bx.psu.edu. In the tools on the left of the screen, just type manhattan into it to get the right tool. It gives you an explanation of what format the file needs to be in (chromosome number, chromosome bp position, p-value) in a text file exported from excel. Then go to Get Data in the main tool menu and upload the text file from your computer and select it in the Manhattan plotter tool.

Hope that helps,

~ Nick

[Jim Robinson]

Hi,

Apologies for the delayed response.   I think all you will need to do is rename some column headers, then export (save)  your data as "tab-delimited text",  and name the file so it ends with ".gwas".   Then load it into IGV from the file menu.    Required columns are described in the link below

http://www.broadinstitute.org/software/igv/GWAS

Note that the 4 required column headers (CHR, BP, SNP, and P) are case-sensitive.  I think this format comes from PLINK.

Jim

[Katherine Shortt]

Thanks!  I will try this.

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[Jim Robinson]

OK, if that doesn't work email a small example of your excel file to
igv-...@broadinstitute.org. Gwas is not a major component of IGV, but
the manhattan plot should work.