created by bhanuGandham
on 2019-04-16
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`