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Can you use SelectVariants with a combined vcf to produce a new vcf containing only variants present in a particular sample eg. you can select out de novo mutations from a combined family vcf?
Yes, you can do that and much more. Take a look at the documentation: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_SelectVariants.html
Mauricio Carneiro, PhD