Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

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SelectVariants Cookbook Follow

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GATK Team
  • Updated

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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