lgn
New Member
Posts: 1
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Post by lgn on Nov 7, 2016 0:27:23 GMT
Hello.
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.
I am running the following code:
gcta64 --bfile $PROJ_CODE --make-grm --autosome --out $PROJ_CODE
But receive the following error: version 1.26.0 Reading PLINK FAM file from [$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?
Thanks in advance. Leandro
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ying
New Member
Posts: 2
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Post by ying on May 10, 2019 16:45:48 GMT
Hi Leandro,
I have the same issue. Have you solved the problem yet?
Thanks! Ying
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hcj
New Member
Posts: 1
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Post by hcj on Jan 27, 2022 21:07:43 GMT
Hi both,
I am trying to do the same thing. Did you have any luck?
Thanks!
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