Conerting vcf to 23andMe format
1
2
Entering edit mode
8.5 years ago
kvs ▴ 20

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

next-gen snp • 6.0k views
ADD COMMENT
3
Entering edit mode
8.5 years ago
plink --vcf [vcf filename] --recode 23
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

use :

bcftools norm 

to split from multiallelic to single one

Source: bcftools

ADD REPLY

Login before adding your answer.

Traffic: 2501 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6