I have about 30 different GWAS results with z-scores and I'm trying to apply ImpG to each of studies. I noticed that I can use the same haps/ and maps/ for all these traits. My workflow is done 4.2.1, 4.2.2, 4.2.3 once and repeat 4.2.4.2, 4.2.5, 4.2.6 and 4.2.7 for 30 different GWAS results.
I noticed that it takes more than 3 days for step 4.2.5 to complete for the larger chromosomes. I'm wondering if I can use the same beta file for all the GWAS results. In other words, can I complete step 4.2.5 one time and use the same beta output for rest of the GWAS results? By the way, what is the output of the GenBeta command? It looks like a SNPxSNP matrix, but I'm not sure what the values are.
I have about 30 different GWAS results with z-scores and I'm trying to apply ImpG to each of studies. I noticed that I can use the same haps/ and maps/ for all these traits. My workflow is done 4.2.1, 4.2.2, 4.2.3 once and repeat 4.2.4.2, 4.2.5, 4.2.6 and 4.2.7 for 30 different GWAS results. I noticed that it takes more than 3 days for step 4.2.5 to complete for the larger chromosomes. I'm wondering if I can use the same beta file for all the GWAS results. In other words, can I complete step 4.2.5 one time and use the same beta output for rest of the GWAS results? By the way, what is the output of the GenBeta command? It looks like a SNPxSNP matrix, but I'm not sure what the values are.