"Error: --recode 23 cannot be used with multi-character allele names." when converting VCF to 23andme

Question

[beneficii]

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?

Answer 1

[nuria.mauri]

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

[chrchang523]

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