Hi,
I am new to GWAS. I have dataset of 15K+ individuals and 200+ SNPs. I wanted to estimate the relatedness matrix, I used the following command.
gemma -bfile data_QC -gk 1 -o data_QC_gem
GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020
Reading Files ...
number of total individuals = 15628
number of analyzed individuals = 2904
number of covariates = 1
number of phenotypes = 1
number of total SNPs/var = 270047
number of analyzed SNPs = 260663
Calculating Relatedness Matrix ...
======= 15%
It's been running for 4+ hours.
How much time it will take to complete?
Does it depend on computational resources on my machine?
Any help in this regard would be appreciated.
Thank you
Hi, I am new to GWAS. I have dataset of 15K+ individuals and 200+ SNPs. I wanted to estimate the relatedness matrix, I used the following command.
gemma -bfile data_QC -gk 1 -o data_QC_gem
GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020 Reading Files ...
number of total individuals = 15628
number of analyzed individuals = 2904
number of covariates = 1
number of phenotypes = 1
number of total SNPs/var = 270047
number of analyzed SNPs = 260663
Calculating Relatedness Matrix ... ======= 15%
It's been running for 4+ hours. How much time it will take to complete? Does it depend on computational resources on my machine? Any help in this regard would be appreciated. Thank you