Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

SelectVariants Cookbook

bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

how to use SelectVariants to find common variants:

gatk SelectVariants \ -V gs://gatk-tutorials/workshop_1702/variant_discovery/data/inputVcfs/trio.vcf.gz \ -select 'vc.getGenotype("NA12878").isHomRef()' -select 'vc.getGenotype("NA12877").isHomRef()' -select 'vc.getGenotype("NA12882").isHomRef()' \ --invertSelect true \ -O /home/jupyter-user/motherSNP.vcf.gz

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