converting genotype file to vcf
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Entering edit mode
3.5 years ago
sm15766 • 0

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 • 1.6k views
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Entering edit mode

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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