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converting genotype file to vcf

hi,

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.

thanks.

snp vcf
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written by sm15766 • sm15766

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!

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written by Matteo Schiavinato Matteo Schiavinato

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