How to run on a GWAS summary statistics dataset

[skr3178]

Hi,

Thank you for providing this tool.
I would liek to use it for the dataset presented here: https://ctg.cncr.nl/software/summary_statistics/
(dataset: AD_sumstats_Jansenetal_2019sept.txt.gz ).

I think I am missing the config file and the SNP file.
Probably I can copy the config file from the default/tutorial model. But how to get the SNP data? Is it possible to do a ManhPLot on this dataset or am I missing somehting?

[cgrace1978]

Thanks for your message. The information regarding formatting of input data is provided here:

https://github.com/cgrace1978/manhplot/wiki#input-files

You need to do the following:

1. Format the AD_sumstats_Jansenetal_2019sept.txt.gz data so it conforms with GWAS input file
2. For the list of SNPs these are the significant SNPs from the GWAS - so you need to get this from the Jansen 2019 paper.
3. You can use the config file provided. But see the wiki page for instructions on how this is formatted.

Thanks,

Chris Grace