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Select Variants based on treatments and replicates

Hi GATK,

Thanks to you, we've got an amazing .vcf file just bursting with SNPs. If my file contains five replicates of a control group and five replicates of a treatment group (so 10 individuals total) and I'd like to select variants which are the same across all members of the control group, the same across all members of the replicate group, but different between the two groups, can I accomplish that with SelectVariants and JEXL? Or via some even easier method?

Thanks for your time. Please feel free to rather curtly request a clarification if I've garbled my question.

Aloha,

Brian

Answers

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