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compare genotypes in two vcf files

Hi All,

What is the best way to compare genotypes between two different vcf files.

Thanks
Tarek

vcf genotype
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updated by Ram Ram • written by tarek.mohamed tarek.mohamed

how many sample per vcf ? is it the same samples ?

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written by Pierre Lindenbaum Pierre Lindenbaum

Hi Pierre,

I have only one sample per vcf file. Basically, I has genotype calls from illumina final report, then I converted them to ped then to vcf files.

Thanks Tarek

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written by tarek.mohamed tarek.mohamed

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