Re: [Vcftools-help] How to obtain the difference of two VCF files

[Ryan G. <gol...@um...>]

Ah, nevermind.  I see vcf-isec does this.

On 5/27/11 12:10 PM, Ryan Golhar wrote:
> Hi - I have generated a VCF file for two individuals using GATK for a
> select set of genes.  I now want to obtain a VCF file containing just
> the SNPs in one individual and not the other.  I thought vcftools --diff
> would do this, but it doesn't, or I'm not using it correctly.
>
> Is there a way to subtract one VCF file from another to get a VCF file
> contain just the SNPs unique to one of the samples?
>

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