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We are running GATK HaplotypeCaller on ~50 whole exome samples. We are interested in rare variants - so we ran GATK in single sample mode instead of multi sample as you recommend, however we would like to take advantage of VQSR. What would you recommend? Can we run VQSR on the output from GATK single sample?
Additionally, we are likely to run extra batches of new exome samples. Should we wait until we have them all before running them through the GATK pipeline?
Many thanks in advance.