Conerting vcf to 23andMe format
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5.9 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 • 4.3k views
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3
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5.9 years ago
plink --vcf [vcf filename] --recode 23
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looks good, I didn't notice this function before.

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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?

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use :

bcftools norm 

to split from multiallelic to single one

Source: bcftools

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