Hi bioGWAS team,
I tried using your tool to simulate GWAS summary statistics using a set of plink files I had previously created. I ran into an issue during the post-filtering step executed in "snakemake.not_sim_geno.smk". The step is currently trying to use plink to filter the original b-files ("params.bfile"). Shouldn't it be trying to filter the prefiltered outputs generated in the previous step? Those are what's listed as the step's input, but they're not referenced in the shell command.
I apologize if I'm mistaken. However, if I am, please be advised that the script will not run if the original b-files are stored in a different directory than the user-input "--data_dir".
I hope this is useful and thank you for developing bioGWAS!
Hi bioGWAS team,
I tried using your tool to simulate GWAS summary statistics using a set of plink files I had previously created. I ran into an issue during the post-filtering step executed in "snakemake.not_sim_geno.smk". The step is currently trying to use plink to filter the original b-files ("params.bfile"). Shouldn't it be trying to filter the prefiltered outputs generated in the previous step? Those are what's listed as the step's input, but they're not referenced in the shell command.
I apologize if I'm mistaken. However, if I am, please be advised that the script will not run if the original b-files are stored in a different directory than the user-input "--data_dir".
I hope this is useful and thank you for developing bioGWAS!