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GATK Staff

VQSR for single sample exome/targeted regions

I read on the best practices slides that I should not use VQSR if the cohort is small. I only one sample for a single individual. I was wondering how useful it is to perform VQSR on this sample by using the GVCFs from 1000G? Am I losing a lot by not doing VQSR step for a single sample? I have some parameters in mind that I want the final VCF to satisfy: Min Q and Min depth.



Best Answer


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