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hakyimlab / summary-gwas-imputation

harmonization, liftover, and imputation of summary statistics from GWAS
MIT License
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Coloc with GTEx data: WARNING - R[write to console]: Error in process.dataset(d = dataset1, suffix = " dataset df1: Length of snp names and beta vectors must match #11

Closed lauraand1705 closed 3 years ago

lauraand1705 commented 3 years ago

Hi, I am running the below script, but gets this error:

WARNING - R[write to console]: Error in process.dataset(d = dataset1, suffix = "dataset df1: Length of snp names and beta vectors must match

python3 ../summary-gwas-imputation/src/run_coloc.py \ -gwas_mode bse \ -gwas ../metaXcan/meta_harm_200803.tab.gz \ -eqtl_mode bse \ -eqtl ../data/GTEx_Analysis_v8_eQTL/Heart_Atrial_Appendage.v8.egenes.txt.gz \ -gwas_sample_size 32036 \ -eqtl_sample_size 372 \ -parsimony 8 \ -output test > /dev/null

Can you help me with this error message? Best regards, Laura.

Heroico commented 3 years ago

Hi Laura,

Unfortunately this script is undocumented and provided as-is. You would have to debug it with your data. You can use the argument --keep_intermediate_folder, so that you can inspect the internal artifacts fed to coloc's R script src\ncoloc.R by this script.

Best,

Alvaro