Randomly sampling vcf

isp2isp2 Posts: 7Member

When I use SelectVariants -fraction option more than once, I always get the same variant sites. The same happens for RandomlySplitVariants. Is there a way of randomly taking a fraction of the vcf that is not always the same, but truly random (which means it will pick different sites each time, of course with a certain probability of including common sites)?

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,401Administrator, GATK Developer admin

    That should do the trick.

    Geraldine Van der Auwera, PhD

  • isp2isp2 Posts: 7Member

    Yes, it does. Thank you!

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