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gusevlab / fusion_twas

methods for functional summary-based imputation
http://gusevlab.org/projects/fusion/
GNU General Public License v3.0
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coloc analysis still broken, even on earlier versions #61

Open Chris-Wills opened 1 year ago

Chris-Wills commented 1 year ago

I am running the following command:

Rscript ../../FUSION/FUSION.assoc_test.R \
        --sumstats "$sumstats" \
        --weights "$weights" \
        --weights_dir "$weights_dir" \
        --ref_ld_chr "$ref_ld_chr" \
        --chr "$i" \
        --coloc_P 0.001 \
        --PANELN "$weights" \
        --GWASN 6697 \
        --out "$out"

When --coloc_P is removed everything runs smoothly, when it is added NA is returned for everything. I tried using coloc package versions 5.1.0.1 and 5.1.0 as suggested in previous posts but nothing has changed.

Chris-Wills commented 1 year ago

Rolling back all the way to coloc v3.2-1 fixed it.