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Post by Gabriel on Aug 6, 2014 12:45:28 GMT
Hi,
I want to use my PLINK files for gcta but get the following error message:
Error: Duplicate SNP name found: "AX-83382164"
The snp ids in our file correspond to codes provided to us by Affymetrix. The AX code here is the first snp ID in our file (there are no duplicates). Am I getting this error because GCTA does not recognize these codes (i.e. it expects rs numbers)? Is there a different reason?
Gabe
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Post by Gabriel on Aug 13, 2014 15:28:02 GMT
Perhaps this is too basic of a question and I am missing something, since I have received no replies?
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Post by Jian Yang on Aug 16, 2014 12:11:32 GMT
GCTA doesn't recognise any SNP ID. It accepts any kinds of SNP names. This error message simply means that this name appears at least twice in the file.
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Post by Zhihong Zhu on Sept 2, 2014 13:12:53 GMT
The SNP may have multiple alleles, ie. 3 alleles. Please check the SNPs with this id in bim file.
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Post by willgilks on Nov 19, 2015 10:12:43 GMT
I'm getting the same error message. Notably the offending SNP is the last on the X (23) chromosome:
Options:
--autosome-num 4
--bfile lhm_allcall
--reml
--grm lhm_allcall_grm
--pheno lhm_fitness_gcta.txt
--reml-pred-rand
--out lhm_allcall
Note: This is a multi-thread program. You could specify the number of threads by the --thread-num option to speed up the computation
Reading PLINK FAM file from [lhm_allcall.fam].
222 individuals to be included from [lhm_allcall.fam].
Reading PLINK BIM file from [lhm_allcall.bim].
82055 SNPs to be included from [lhm_allcall.bim].
Error: Duplicated SNP IDs found: "hc_cxmik".
-bash-4.1$ grep -c "hc_cxmik" lhm_allcall.bim
1
And it's biallelic in the bim file, the genotypes file was previously filtered to include only biallelic.
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