I have a vcf file (format VCFv4.0), generated by GATK pipeline starting from Illumina reads. 

I need to convert it to 23andme file format. Example of the 23andme format:

    # rsid  chromosome  position    genotype
    
    rs4477212   1   82154   TT
        
    rs3094315   1   752566  TC
        
    rs3131972   1   752721  AA
        
    rs12124819  1   776546  AC

I am having problems with plink2 `--recode 23 cannot be used with multi-char alleles`. Plink was recommended earlier here https://www.biostars.org/p/198034/#274523 

I tried then to modify the vcf to remove multi-char alleles using [VcfMultiToOneAllele,][1] which did a great job but the output file, even though it looks like a vcf, it was not recognised as such by plink2 `no genotype data in .vcf file`. Any other tool up to the task?

Thanks for any help. 


  [1]: https://lindenb.github.io/jvarkit/VcfMultiToOneAllele.html
OK, it seems I have solved it using: 

    plink2 --vcf [vcf file] --snps-only --recode 23 
now thinking how to include single point deletions and insertions to the output file, because those are missing 
