I am using your tutorial. I am having issues when calculating heritability based on rare variants ( maf >= 0.0001 & maf < 0.001 among 4 cohorts with unrelated sample sizes of 12k). I could able to generate GRM for Q1, When I am running it for Q2/Q3/Q4, I am having issues with GRM generation.
I am using this code to generate the GRM but for some reason, I couldn't able to see any output generated even though the code was successfully run. I used the same code for Q1 and it worked perfectly fine. I am not sure how to deal with this issue.
Code: gcta-1.94.1 --bfile cat1_hqp_q2 --make-grm-part 3 1 --make-grm-alg 1 --thread-num 10 --out cat1_hqp_q2_v1.part_1
Variants input for GRM creation is 8.5m variants across 12k individuals.
Hello,
I am using your tutorial. I am having issues when calculating heritability based on rare variants ( maf >= 0.0001 & maf < 0.001 among 4 cohorts with unrelated sample sizes of 12k). I could able to generate GRM for Q1, When I am running it for Q2/Q3/Q4, I am having issues with GRM generation.
I am using this code to generate the GRM but for some reason, I couldn't able to see any output generated even though the code was successfully run. I used the same code for Q1 and it worked perfectly fine. I am not sure how to deal with this issue.
Code: gcta-1.94.1 --bfile cat1_hqp_q2 --make-grm-part 3 1 --make-grm-alg 1 --thread-num 10 --out cat1_hqp_q2_v1.part_1 Variants input for GRM creation is 8.5m variants across 12k individuals.
Can you help me out with the issue?