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Setting BOTH or POOLBOTH for HaplotypeCaller for multiple individuals of a population?
I'd like to feed HaplotypeCaller with several BAM files for different individuals of a population simultaneously, but I need to genotype alleles for each individuals. Which option do I need set -glm with, BOTH or POOLBOTH?
Another question, I've known GATK won't consider BAQ for calling indels, but when I set -glm with BOTH, if GATK will also turn off BAQ for SNP calling?