Thanks for making GCTA available. I am running an analysis with a non-model species where I have about 300K SNPs located on about 30K unlinked scaffolds. Therefore, there is no information about chromosome and I am not being able to run gcta. I could not find a similar thread on this board, so I appreciate if you could point me to it or help me use gcta under these conditions.
But receive the following error: version 1.26.0 Reading PLINK FAM file from [$PROJ_CODE.fam]. 64 individuals to be included from [$PROJ_CODE.fam]. Reading PLINK BIM file from [$PROJ_CODE.bim]. 1 SNPs to be included from [$PROJ_CODE.bim]. 0 SNPs from chromosome 1 to chromosome 22 are included in the analysis.
Error: No SNP is retained for analysis.
I can run associations with this dataset on plink adding commands --allow-extra-chr --allow-no-sex. Is there something similar in gcta?