Removing SNPs in linkage -> ld.filter?

[Mark]

Hi

I would like to filter out SNPs from a GWAS logistic output file that
are in linkage with SNPs on a predefined list (previously identified
hits) based on an r-squared threshold.

The ld.filter module seems like it might do this, but the syntax in
the documentation is a little unclear to me. I'm not sure, for
example, where to put the reference SNP (or list of SNPs) that I want
to compare. Can you tell me if GLU can do this, and if so, would you
be able to provide an example of the command?

Thanks
Mark

[Jacobs, Kevin (NIH/NCI) [C]]

Hi Mark,

 

I'm happy to help.  The programs have evolved faster than the documentation.  Here is how to run it to accomplish what you desire:

 

Input files:

 

1.      known GWAS hits: knownhits.lst

2.      association results: results.txt

3.      genotypes used for LD: genotypes.lbat  (most any format will work)

 

Run:

 

glu ld.surrogates results.txt --haystack=knownhits.lst genotypes.lbat -o surrogates.txt

 

The SNPs listed without a surrogate are not known hits or in LD with one or more known hit. 

 

-Kevin

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