"Error: --recode 23 cannot be used with multi-character allele names." when converting VCF to 23andme
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4.1 years ago
beneficii ▴ 60

I'm trying to convert a VCF file to a 23andme file. I run VCFTools to convert it to TPED. But then when I run plink1.9 to convert it to 23andme, I get the following error:

"Error: --recode 23 cannot be used with multi-character allele names."

What should I do?

vcftools plink1.9 • 1.9k views
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2.4 years ago

a bit late but ... That's because current plink can not manage indels, then, only one base is allowed at ref or alt field. Try to add this: --snps-only

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Actually, plink can handle indels, it's the 23andMe format which can't really represent them.

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