GATK Best practices linked below glosses over alignments, which are obviously required to follow the steps in the guide. You can use any of the many NGS aligners available (BBMap, BWA, Bowtie2, if you are doing genome alignments) (BBMap, STAR, HISAT2 if you need a splice-aware aligner). Pick an aligner and then stick with it, once you understand its options (there are many for most and they are all program specific). You would also need access to a reference genome and will have to create search indexes (that are again aligner specific).

Have a look at the GATK best practices.