Question: converting genotype file to vcf
gravatar for sm15766
17 months ago by
sm157660 wrote:


I have some data in the format

    113934  126070
Individual1 0   0
Individual1 0   0
Individual2 0   0
Individual2 1   0
Individual3 0   0
Individual3 0   0
Individual4 0   0
Individual4   0     1

etc, with each column a SNP and each 2 rows haplotype from an individual. I'd quite like to convert this to VCF format, where the first individual would be represented by (1,0,0) (homozygous for reference).

Does anyone know of any scripts to do this, as I'm not sure I'm up to making one myself.


snp vcf • 801 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by sm157660

You mean converting this genotype file to the VCF-formatted genotype, right? Because if you want a whole VCF line, you miss some information!

EDIT: individual 4 has only 1 line!

ADD REPLYlink modified 17 months ago • written 17 months ago by Macspider2.8k
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