Post by jramirezdiaz on Aug 1, 2022 20:12:07 GMT
Hi everyone
I am still quite new to GCTA.
I've been trying to run the GWAS analysis for disease trait (binary) in sheep
The two first command-line seems to be running fine: "gcta64 --bfile less-ld-sheep --make-grm --autosome-num 26 --thread-num 10 --out geno_grm"
"gcta64 --grm geno_grm --autosome-num 26 --make-bK-sparse 0.05 --out sp_grm"
However, when I try to run the 3 line ("gcta64 --bfile less-ld-sheep --grm-sparse sp_grm --fastGWA-mlm-binary --pheno pheno_gcta1.txt --qcovar cov_gcta3.txt --thread-num 10 --out geno_assoc"), I get the following message; Error: invalid option "--grm-sparse"
It seems that the "--grm-sparse" option does not register
I've also tried using the mbfile option, but I'm not sure if the file input is correct, is it necessary to separate each chr and create a list? Using the mbfile doesn't work either
Thanks in advance for any help,
Jramirezdiaz
I am still quite new to GCTA.
I've been trying to run the GWAS analysis for disease trait (binary) in sheep
The two first command-line seems to be running fine: "gcta64 --bfile less-ld-sheep --make-grm --autosome-num 26 --thread-num 10 --out geno_grm"
"gcta64 --grm geno_grm --autosome-num 26 --make-bK-sparse 0.05 --out sp_grm"
However, when I try to run the 3 line ("gcta64 --bfile less-ld-sheep --grm-sparse sp_grm --fastGWA-mlm-binary --pheno pheno_gcta1.txt --qcovar cov_gcta3.txt --thread-num 10 --out geno_assoc"), I get the following message; Error: invalid option "--grm-sparse"
It seems that the "--grm-sparse" option does not register
I've also tried using the mbfile option, but I'm not sure if the file input is correct, is it necessary to separate each chr and create a list? Using the mbfile doesn't work either
Thanks in advance for any help,
Jramirezdiaz