Hello,

I have a general question regarding the difference between MergeVcfs and SortVcf. From my understanding, after reading the documentation, they both work similarly? Both tools can accept more than one input vcf file, both tools requires that identical samples be present if using more than one file as input, and both tools provide an output that is sorted by coordinate. Am I understanding this correctly? Is there any difference behind the scenes as to how two vcf files (ie. one with SNPs and another with INDELs) containing the same set of samples would be combined with either tool?

Appreciate any insight on this. Thanks

a) GATK version used: 4.6.1.0