Post by johan on May 17, 2024 9:14:39 GMT
Hi all, I am trying to run single and bivariate GCTA on our Linux computation cluster but can't seem to get the right output file. GCTA is supposed to produce a .hsq -file, but it is missing after completing the analysis. Has anyone else experienced this issue?
Example of my command for single reml:
Example of my command for bivariate reml:
Then while I am here, I wanted to ask about how GCTA deals with LD in its method, while not relying on an external LD reference as for example LDSC. I am guessing it is always using the LD pattern of the provided bfiles. Would it be an idea to be able to provide an external LD panel (which may be obtained from WGS rather than genotyping), for example 1kG, to use for only LD calculations, while still using the other/standard bfile for the variance constructions or GWAS?
Kind regards,
Johan
Example of my command for single reml:
gcta64 --bfile mybfiles --grm mygrm.grm --pheno myphen.phen --qcovar covar.q.txt --covar covar.c.txt --keep keep.all.txt --thread-num 10 --reml --out sim1ldExample of my command for bivariate reml:
gcta64 --reml-bivar --bfile mybfiles --grm mygrm.grm --pheno myphen.phen --qcovar covar.q.txt --covar covar.c.txt --keep keep.all.txt --thread-num 10 --out sim1and2ldThen while I am here, I wanted to ask about how GCTA deals with LD in its method, while not relying on an external LD reference as for example LDSC. I am guessing it is always using the LD pattern of the provided bfiles. Would it be an idea to be able to provide an external LD panel (which may be obtained from WGS rather than genotyping), for example 1kG, to use for only LD calculations, while still using the other/standard bfile for the variance constructions or GWAS?
Kind regards,
Johan