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Advice for running GenotypeVCF and Recalibration on a thousand samples

shubhamsainishubhamsaini UCSDMember
edited April 2017 in Ask the GATK team

Hi,

I am working with a couple thousand gVCFs. I plan to run GenotypeGVCF and ApplyRecalibration on them in a joint fashion. I want to know how does GATK scale on these numbers, and is it even recommended to run this analysis on these numbers?

I tried running GenotypeGVCF in multi-threaded mode, but it runs into race condition (or some other issue) and a single thread seems the only viable option.

Answers

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