Conerting vcf to 23andMe format

Question

[kvs]

Is there any way can we convert a vcf file to 23andMe format? The format is given below. rsids have been incorporated to the ID column of the vcf file. Here is the format output exptected

 # rsid  chromosome  position    genotype

rs4477212   1   82154   TT

rs3094315   1   752566  TC

rs3131972   1   752721  AA

rs12124819  1   776546  AC

rs11240777  1   798959  GA

rs6681049   1   800007  CC

Similar questions are not been addressed in any of the online forumn. Please help

Answer 1

[chrchang523]

plink --vcf [vcf filename] --recode 23

[jimmy_zeng]

looks good, I didn't notice this function before.

[alec_djinn]

I am having problems with plink2 --recode 23 cannot be used with multi-char alleles. I tried then to modify the vcf to remove multi-char alleles using VcfMultiToOneAllele, which did a great job but the output file, even though it looks like a vcf, it was not recognized as such by plink2 no genotype data in .vcf file. Any other tool up to the task?

[adriano.demarino]

use :

bcftools norm 

to split from multiallelic to single one

Source: bcftools