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When converting vcf to tbed/tfam format, I am getting error like

unrecognized flag<'--transpose'>

Code I used:

plink2 --vcf sample_vcf_file.vcf --recode --transpose --out outputfile
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Correct command is

plink2 --vcf sample_vcf_file.vcf --recode transpose --out outputfile

vcftools also can convert vcf into tped/tfam

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  • $\begingroup$ Yep, from plink manual: --transpose Deprecated. Use "--recode transpose".. $\endgroup$
    – Kamil S Jaron
    Aug 29 '21 at 21:07

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