SelectVariants Cookbook
Solutions to Problems | Created 2019-04-16


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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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