I'm new to GATK and I have 3 vcf files from 3 different individuals: mother.vcf, father.vcf, and child.vcf. I want to obtain a single vcf file that would have all the variants of each individual in order to analyze the trio. After looking online, I learned that GATK has CombineVariants and MergeVcfs that are supposed to combine/merge the vcf files. However, I do not understand which tool is better for my task.
GATK version used: gatk-188.8.131.52
Thank you in advance!
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