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zhengxwen / SNPRelate

R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)
http://www.bioconductor.org/packages/SNPRelate
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Ids in plink bed are not unique #63

Open zillurbmb51 opened 5 years ago

zillurbmb51 commented 5 years ago

Hello, I am using SNPRelate to investigate my variants. When I run: snpgdsBED2GDS(bed_r1321,bim_r1321,fam_r1321,'r1321.gds',cvt.snpid = 'auto') I am getting this:

Start file conversion from PLINK BED to SNP GDS ...
    BED file: '1321.maf5.indep0.1.bed'
        SNP-major mode (Sample X SNP), 2.4M
Error in snpgdsBED2GDS(bed_r1321, bim_r1321, fam_r1321, "r1321.gds", cvt.snpid = "auto") : 
  IDs in PLINK BED are not unique!

Any Help? Best, Zillur

zhengxwen commented 5 years ago

Please check and modify your fam file. It says "family ID + individual ID" is not unique.

zillurbmb51 commented 5 years ago

Ok. Thank you very much. Here is my fam file and how can I edit this? Best, Zillur 1321.maf5.indep0.1.fam.txt