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ghm17 / LOGODetect

LOGODetect is a powerful tool to identify small segments that harbor local genetic correlation between two traits/diseases.
GNU General Public License v3.0
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Which sumstats file to pass to LDSC? #6

Closed jdblischak closed 3 years ago

jdblischak commented 3 years ago

In Step 1, the two original sumstats files are preprocessed to create output_dir/Data_QC/dat1.txt and output_dir/Data_QC/dat2.txt (and the per chromosome files). Then in Step 2, the original sumstats files are passed to the LDSC argument --sumstats. Shouldn't the preprocessed sumstats files be passed to LDSC? I realize that in the tutorial example these files are identical (i.e. preprocess.R has no effect), but if it did filter some SNPs or flip some alleles and effect sizes, shouldn't they be used?

ghm17 commented 3 years ago

In practice, LDSC will also preprocess the sumstats files to give reliable heritability and genetic covariance estimates. Therefore, LDSC will give similar results either the original sumstats files or the preprocessed sumstats files are passed to argument --sumstats. Yet I agree that it would be more straightforward passing the preprocessed sumstats files to LDSC.