GREML calculation with GCTA

CNSGenomics / Heritability_WGS

This repository contains the code used for estimating heritability from WGS data

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GREML calculation with GCTA #1

Open dianacornejo opened 2 years ago

dianacornejo commented 2 years ago

Hi, I wonder if you run into memory issues when trying to calculate the the REML using the GRM in GCTA. I keep getting errors and I was wondering weather you can use a sparse GRM instead of the *.grm.bin. Is your code in GRM manipulation precisely to reduce the number of individuals so that GCTA can deal with it. Thanks a lot

WPierrick commented 2 years ago

Hi, yes GREML-LDMS can require a lot of memory. You need full GRMs for the analysis. What error do you get, what is your sample size, how many GRMs are you fitting and how much memory are you requiring? No, the code is for extract and manipulate GRM elements directly (not recomended in your case), you want to use -grm-cutoff to remove related samples.