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jianyangqt / gcta

GCTA software
GNU General Public License v3.0
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Inquiry about the LD window size setting in the GSMR via GCTA tool #81

Closed laleoarrow closed 4 months ago

laleoarrow commented 4 months ago

Hi all, I see that there is --clump-r2 0.05 flag to set the r2 cutoff but I did not found the flag to set LD window size. Does the window size setting for clumping in GSMR are not changeable? If so, what is the default setting? (e.g., 1MB? 500KB?)

anglixue commented 4 months ago

Hi, You can use flag clump_wind_size to change the clumping LD window size. The unit is kb and the default setting is 1000 (i.e., 1Mb). Let me know if it works for you. Thanks!

Angli

laleoarrow commented 4 months ago

This should get me going! Thank you for clarifing this!

pjawinski commented 1 week ago

Hi everyone,

I was exploring the options for the precompiled Linux executables and discovered that the flag --clump-kb can be used to modify the default window size for clumping. This flag overwrites the internal clump_wind_size variable. The default value of clump_wind_size is 10000 (i.e., 10Mbp) as set for mtCOJO in main/option.cpp (line 168, see also 1186-1190). In my testing, I found that using--clump-kb 10000 produces the same results as omitting the flag, confirming that this is indeed the default behavior.

Just thought I'd share in case anyone else finds it useful!